From 2210b03b01965507a9a1146c39e205876fc25a10 Mon Sep 17 00:00:00 2001
From: Eduard Kerkhoven <eduardk@chalmers.se>
Date: Sat, 11 Jul 2026 02:17:12 +0200
Subject: [PATCH 1/6] fix: couple non-ETF flavoenzymes to ubiquinone instead of
 the ETF pathway (#1015)

MAR06911 (EC 1.5.5.1) represents the ETF:ubiquinone oxidoreductase (ETFDH)
step that reoxidises the matrix FADH2 pool. Its gene rule had accumulated
into an 'or' of nine genes, six of which encode flavoenzymes that reduce
ubiquinone directly and do not use ETF: GPD2, PRODH, PRODH2, CHDH, DHODH
and SQOR (Banerjee et al. 2022, FEBS J, PMID:34428349). This caused two
artefacts, most visible in enzyme-constrained (GECKO) models:
- all FADH2-to-ubiquinone flux was constrained by the single ETFDH kcat,
  so e.g. the glycerol-3-phosphate shuttle was constrained twice;
- beta-oxidation electrons could reach the ETC without ETFDH (via the GPD2
  branch of the 'or' rule), which is biologically incorrect.

Changes:
- Restore MAR00483 (sn-glycerol-3-phosphate:ubiquinone oxidoreductase,
  GPD2, EC 1.1.5.3); remove FAD-linked MAR00449 and its Recon3D duplicate
  MAR01169.
- Restore MAR03838 (L-proline:ubiquinone oxidoreductase, PRODH/PRODH2);
  remove FAD-linked MAR08611 (PRODH electron transfer to ubiquinone:
  Tanner 2018, PMID:28990412).
- Set the MAR06911 gene rule to the ETF system only,
  "ENSG00000105379 and ENSG00000140374 and ENSG00000171503"
  (ETFB and ETFA and ETFDH), matching the and-joined convention used for
  the other obligate ETC complexes.

DHODH already reduces ubiquinone through its own reaction (MAR20167) and
needs no further change. CHDH (MAR08441) and SQOR (MAR20186) still deposit
electrons in the matrix FADH2 pool and should be given direct ubiquinone
reactions in a follow-up. Removed reactions are recorded in
deprecatedReactions.tsv.
---
 .../deprecatedReactions.tsv                   |  4 ++
 model/Human-GEM.yml                           | 44 ++++++-------------
 model/reactions.tsv                           |  7 ++-
 3 files changed, 21 insertions(+), 34 deletions(-)

diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
index b48534b3..bfb897b4 100644
--- a/data/deprecatedIdentifiers/deprecatedReactions.tsv
+++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -401,3 +401,7 @@ MAR07851		DNDPt62m				DNDPt62m	MNXR97327	HMR_7851	RCR20193		0			HMR_7851
 MAR07852		DNDPt63m				DNDPt63m	MNXR97676	HMR_7852	RCR20146		0			HMR_7852
 MAR07853		DNDPt6m				DNDPt6m	MNXR97677	HMR_7853	RCR20194		0			HMR_7853
 MAR07854		DNDPt7m				DNDPt7m	MNXR97175	HMR_7854	RCR20122		0			HMR_7854
+
+MAR08611	R10507	PROD2m		r1453		PROD2m	MNXR103187	HMR_8611;HMR_3838	RCR11294;RCR14286		0			HMR_8611;HMR_3838;MAR03838
+MAR00449	R00848;R00849			r0205	R-HSA-188467	GLYC3PFADm;r0205	MNXR99875;MNXR106713	HMR_0449;HMR_0483	RCR12494;RCR21050		0		RHEA:31283;RHEA:18977	HMR_0449;HMR_0483
+MAR01169	R00849;R00848	G3PD2m	R00848C	r0205		G3PD2m;r0205;HMR_0482	MNXR99878;MNXR106713;MNXR192664	HMR_0483;HMR_0482	RCR21050;RCR14578		0		RHEA:18977	G3PD2m;HMR_0483;HMR_0482;MAR00482;MAR00483
\ No newline at end of file
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
index 5dc46667..bbcd3adc 100644
--- a/model/Human-GEM.yml
+++ b/model/Human-GEM.yml
@@ -70453,20 +70453,20 @@
       - subsystem: "Arginine and proline metabolism"
       - confidence_score: 0
     - !!omap
-      - id: "MAR08611"
-      - name: "L-proline:(acceptor) oxidoreductase"
+      - id: "MAR03838"
+      - name: "L-proline:ubiquinone oxidoreductase"
       - metabolites: !!omap
           - MAM00559m: 1
-          - MAM01802m: -1
-          - MAM01803m: 1
           - MAM02039m: 1
           - MAM02770m: -1
+          - MAM03102m: 1
+          - MAM03103m: -1
       - lower_bound: 0
       - upper_bound: 1000
       - gene_reaction_rule: "ENSG00000100033 or ENSG00000250799"
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.5.5.2"
-      - references: "PMID:18506409"
+      - references: "PMID:18506409;PMID:28990412"
       - subsystem: "Arginine and proline metabolism"
       - confidence_score: 0
     - !!omap
@@ -83461,7 +83461,7 @@
           - MAM03103m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000016391 or ENSG00000100033 or ENSG00000102967 or ENSG00000105379 or ENSG00000115159 or ENSG00000137767 or ENSG00000140374 or ENSG00000171503 or ENSG00000250799"
+      - gene_reaction_rule: "ENSG00000105379 and ENSG00000140374 and ENSG00000171503"
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.5.5.1"
       - references: "PMID:34428349"
@@ -101768,20 +101768,20 @@
       - subsystem: "Acylglycerides metabolism"
       - confidence_score: 0
     - !!omap
-      - id: "MAR00449"
-      - name: "sn-Glycerol-3-phosphate:(acceptor) 2-oxidoreductase"
+      - id: "MAR00483"
+      - name: "sn-glycerol-3-phosphate:ubiquinone oxidoreductase"
       - metabolites: !!omap
-          - MAM01690m: 1
-          - MAM01802m: -1
-          - MAM01803m: 1
-          - MAM02914m: -1
+          - MAM01690c: 1
+          - MAM02914c: -1
+          - MAM03102m: 1
+          - MAM03103m: -1
       - lower_bound: 0
       - upper_bound: 1000
       - gene_reaction_rule: "ENSG00000115159"
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.1.5.3"
-      - references: "PMID:11955283;PMID:2115809;PMID:2923620;PMID:3338458;PMID:340460;PMID:8401296;PMID:8549872;PMID:8579375;PMID:9171333;PMID:9244403;PMID:9559543;PMID:7821823;PMID:8687421;PMID:8163052"
-      - subsystem: "Acylglycerides metabolism"
+      - references: "PMID:11955283;PMID:2115809;PMID:2923620;PMID:3338458;PMID:340460;PMID:8401296;PMID:8549872;PMID:8579375;PMID:9171333;PMID:9244403;PMID:9559543"
+      - subsystem: "Glycerophospholipid metabolism"
       - confidence_score: 0
     - !!omap
       - id: "MAR00604"
@@ -187812,22 +187812,6 @@
       - references: "PMID:10386598"
       - subsystem: "Blood group biosynthesis"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR01169"
-      - name: "Glycerol-3-Phosphate Dehydrogenase (FAD), Mitochondrial"
-      - metabolites: !!omap
-          - MAM01690c: 1
-          - MAM01802m: -1
-          - MAM01803m: 1
-          - MAM02914c: -1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000115159"
-      - rxnFrom: "Recon3D"
-      - eccodes: "1.1.5.3"
-      - references: "PMID:11955283;PMID:2115809;PMID:2923620;PMID:3338458;PMID:340460;PMID:8401296;PMID:8549872;PMID:8579375;PMID:9171333;PMID:9244403;PMID:9559543;PMID:11385633"
-      - subsystem: "Glycolysis / Gluconeogenesis"
-      - confidence_score: 0
     - !!omap
       - id: "MAR01314"
       - name: "GABA Secretion via Secretory Vesicle (ATP Driven)"
diff --git a/model/reactions.tsv b/model/reactions.tsv
index 74283fb5..e144c0a1 100644
--- a/model/reactions.tsv
+++ b/model/reactions.tsv
@@ -632,7 +632,7 @@ MAR08607		UNK2				UNK2	MNXR105128	HMR_8607	RCR10315		0			HMR_8607
 MAR08608	R02894	DRIBt				HMR_8608	MNXR107807	HMR_8608	RCR14308		0	RHEA:78259		HMR_8608
 MAR08609	R01251	P5CRm				P5CRm	MNXR102302	HMR_8609	RCR10244		0	RHEA:14109	RHEA:14109	HMR_8609
 MAR08610	R10507	PROD2				PROD2	MNXR192607	HMR_8610	RCR10316		0			HMR_8610
-MAR08611	R10507	PROD2m		r1453		PROD2m	MNXR192607	HMR_8611;HMR_3838	RCR11294;RCR14286		0			HMR_8611;HMR_3838;MAR03838
+MAR03838	R10507	PROD2m		r1453		PROD2m	MNXR103187	HMR_3838	RCR14286		0			HMR_3838;HMR_8611;MAR08611
 MAR04285	R00713	SSALx	R00713C	r0178		r0178	MNXR104540	HMR_4285	RCR11295		0	RHEA:13218	RHEA:13217	HMR_4285
 MAR00457	R01514	GLYCK	R01514C	r0339		r0339	MNXR100328	HMR_0457	RCR11296		0	RHEA:23517	RHEA:23516	HMR_0457
 MAR00460	R01514	GLYCK	R01514C	r0340		r0340	MNXR100328	HMR_0460	RCR11297		0	RHEA:23517	RHEA:23516	HMR_0460
@@ -2474,7 +2474,7 @@ MAR00001					R-HSA-174757	HMR_0001		HMR_0001	RCR30273		0			HMR_0001
 MAR00002	R02250					HMR_0002		HMR_0002	RCR30274		0			HMR_0002
 MAR00003	R02687					HMR_0003		HMR_0003	RCR30275		0			HMR_0003
 MAR00005	R01351					HMR_0005		HMR_0005	RCR12493		0		RHEA:34019	HMR_0005
-MAR00449	R00848;R00849	G3PD		r0205	R-HSA-188467	GLYC3PFADm;r0205	MNXR192664	HMR_0449;HMR_0483	RCR12494;RCR21050		0	RHEA:31283	RHEA:31283;RHEA:18977	HMR_0449;HMR_0483
+MAR00483	R00848;R00849	G3PD2m	R00848C			G3PD2m	MNXR99878	HMR_0483	RCR21050		0	RHEA:18977		HMR_0449;HMR_0483;MAR00449;MAR01169
 MAR00604	R02240	DAGK_hs				DAGK_hs		HMR_0604	RCR14512		0		RHEA:10272	HMR_0604
 MAR00605	R02251			r1223		HMR_0605		HMR_0605	RCR12495		0		RHEA:10868	HMR_0605
 MAR00665	R02250			r1224		HMR_0665		HMR_0665	RCR14513		0			HMR_0665
@@ -8197,8 +8197,7 @@ MAR01078		FUCFUCGALACGLCGALGLUSIDEtg				FUCFUCGALACGLCGALGLUSIDEtg	MNXR99694
 MAR01083		FUT18g				FUT18g	MNXR99731				0			FUT18g
 MAR01118		FUT34g				FUT34g	MNXR99739				0			FUT34g
 MAR01141		FUT93g				FUT93g	MNXR99751				0			FUT93g
-MAR01169	R00849;R00848	G3PD2m	R00848C	r0205		G3PD2m;r0205;HMR_0482	MNXR99878;MNXR106713;MNXR192664	HMR_0483;HMR_0482	RCR21050;RCR14578		0	RHEA:31283	RHEA:18977	G3PD2m;HMR_0483;HMR_0482;MAR00482;MAR00483
-MAR01314		GABAVESSEC				GABAVESSEC	MNXR137724				0			GABAVESSEC
+MAR01314		GABAVESSEC				GABAVESSEC	MNXR99916				0			GABAVESSEC
 MAR01340		GALFUCGALACGLCGAL14ACGLCGALGLUSIDEtg				GALFUCGALACGLCGAL14ACGLCGALGLUSIDEtg	MNXR99968				0			GALFUCGALACGLCGAL14ACGLCGALGLUSIDEtg
 MAR01348		GALGLUSIDEtg				GALGLUSIDEtg	MNXR99974				0			GALGLUSIDEtg
 MAR01349		GALGLUSIDEtl				GALGLUSIDEtl	MNXR99974				0			GALGLUSIDEtl

From 0f267d897e44045e7c7d557a103ba6827719ae1b Mon Sep 17 00:00:00 2001
From: edkerk <7326655+edkerk@users.noreply.github.com>
Date: Wed, 15 Jul 2026 19:27:09 +0000
Subject: [PATCH 2/6] chore: update model QC results [skip ci]

---
 data/testResults/README.md                     |  6 +++---
 data/testResults/macaw_results.csv             |  7 +++----
 data/testResults/model_qc_summary.md           | 16 ++++++++--------
 data/testResults/qc_annotation_consistency.csv |  2 ++
 4 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/data/testResults/README.md b/data/testResults/README.md
index def0df92..8458c079 100644
--- a/data/testResults/README.md
+++ b/data/testResults/README.md
@@ -4,9 +4,9 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/
 
 The test results shown here were obtained by the GitHub Actions run in:
 
-- **PR #1027** (model QC checks)
-- **PR #1027** (MEMOTE)
-- **PR #1027** (MACAW and mass/charge balance)
+- **PR #1028** (model QC checks)
+- **PR #1028** (MEMOTE)
+- **PR #1028** (MACAW and mass/charge balance)
 - **PR #1027** (gene essentiality)
 
 The results will be updated by any subsequent pull request. Summary results are shown as a comment in the corresponding pull request.
diff --git a/data/testResults/macaw_results.csv b/data/testResults/macaw_results.csv
index 5b8d58da..06a044a4 100644
--- a/data/testResults/macaw_results.csv
+++ b/data/testResults/macaw_results.csv
@@ -632,7 +632,7 @@ MAR08607,MAM01016c + MAM01975c + 2 MAM02039c --> MAM01974c + MAM02471c,ok,ok,ok,
 MAR08608,MAM01742c + MAM02630c --> MAM00558c + MAM02039c + MAM02041c,MAM00558c,ok,ok,ok,N/A
 MAR08609,MAM00559m + 2 MAM02039m + MAM02555m --> MAM02554m + MAM02770m,ok,ok,ok,ok,N/A
 MAR08610,MAM01802c + MAM02770c --> MAM00559c + MAM01803c + MAM02039c,ok,ok,ok,ok,N/A
-MAR08611,MAM01802m + MAM02770m --> MAM00559m + MAM01803m + MAM02039m,ok,ok,ok,ok,N/A
+MAR03838,MAM02770m + MAM03103m --> MAM00559m + MAM02039m + MAM03102m,ok,ok,ok,ok,N/A
 MAR04285,MAM02040m + MAM02552m + MAM02942m --> 2 MAM02039m + MAM02553m + MAM02943m,ok,ok,ok,ok,N/A
 MAR00457,MAM01371c + MAM01982c --> MAM00913c + MAM01285c + MAM02039c,ok,ok,ok,ok,N/A
 MAR00460,MAM01371m + MAM01982m --> MAM00913m + MAM01285m + MAM02039m,ok,ok,ok,ok,N/A
@@ -2474,7 +2474,7 @@ MAR00001,MAM01570e --> MAM01569e + 77243 MAM02956e,ok,ok,ok,ok,N/A
 MAR00002,MAM02040e + MAM02956e --> MAM00234e + MAM01807e,ok,ok,ok,ok,N/A
 MAR00003,MAM00234e + MAM02040e --> MAM00503e + MAM01807e,ok,ok,ok,ok,N/A
 MAR00005,MAM00503c + MAM02040c --> MAM01807c + MAM01983c,ok,ok,ok,ok,N/A
-MAR00449,MAM01802m + MAM02914m --> MAM01690m + MAM01803m,ok,ok,ok,ok,N/A
+MAR00483,MAM02914c + MAM03103m --> MAM01690c + MAM03102m,ok,ok,ok,ok,N/A
 MAR00604,MAM00240c + MAM01371c --> MAM01285c + MAM02039c + MAM02733c,ok,ok,ok,ok,N/A
 MAR00605,MAM00240c + MAM10007c --> MAM01597c + MAM02958c,ok,ok,ok,ok,N/A
 MAR00665,MAM02040c + MAM02958c --> MAM00240c + MAM02039c + MAM10005c,ok,ok,ok,ok,N/A
@@ -8198,7 +8198,6 @@ MAR01078,MAM03578g <=> MAM03578c,only when going backwards,ok,ok,ok,N/A
 MAR01083,2 MAM01950g + MAM03584g --> MAM01856g + 2 MAM01948g + 2 MAM02039g,ok,ok,ok,ok,N/A
 MAR01118,MAM01950g + MAM03092g --> MAM01948g + MAM02039g + MAM03578g,ok,ok,ok,ok,N/A
 MAR01141,MAM01950g + MAM03095g --> MAM01948g + MAM02039g + MAM03577g,ok,ok,ok,ok,N/A
-MAR01169,MAM01802m + MAM02914c --> MAM01690c + MAM01803m,ok,ok,ok,ok,N/A
 MAR01314,MAM00970c + MAM01371c + MAM02040c --> MAM00970e + MAM01285c + MAM02039c + MAM02751c,ok,ok,ok,MAR07738,N/A
 MAR01340,MAM01915g <=> MAM01884c,ok,ok,ok,ok,N/A
 MAR01348,MAM03586c <=> MAM03586g,only when going backwards,ok,ok,ok,N/A
@@ -9365,7 +9364,7 @@ MAR07813,MAM01398r + MAM03109r --> MAM01397r + MAM03106r,ok,ok,ok,ok,N/A
 MAR07817,MAM01627e + MAM02630e --> MAM02039e + MAM02157e,ok,ok,ok,ok,N/A
 MAR07819,MAM03103e <=> MAM03103c,ok,ok,ok,ok,N/A
 MAR07821,MAM01642c --> MAM01642m,ok,ok,ok,ok,N/A
-MAR08111,MAM01690m --> MAM01690c,ok,ok,ok,ok,N/A
+MAR08111,MAM01690m --> MAM01690c,MAM01690m,ok,ok,ok,N/A
 MAR08204,MAM01674e + MAM02040e --> MAM01334e + 2 MAM02039e + MAM02741e,ok,ok,ok,ok,N/A
 MAR08218,MAM01675r + MAM02039r + MAM02555r --> MAM01450r + MAM02554r,ok,ok,ok,ok,N/A
 MAR08274,MAM01371m + MAM01752m --> MAM01285m + MAM01747m,ok,ok,ok,ok,N/A
diff --git a/data/testResults/model_qc_summary.md b/data/testResults/model_qc_summary.md
index 281a485e..04d0a43d 100644
--- a/data/testResults/model_qc_summary.md
+++ b/data/testResults/model_qc_summary.md
@@ -1,6 +1,6 @@
 ## Model quality report
 
-:warning: **6 pre-existing finding(s), no regressions vs `develop`.** Non-blocking.
+:x: **2 regression(s) vs `develop`** (this pull request increased a finding count). Review the :x: rows.
 
 ### Structural checks
 _Duplicate keys (model unloadable) and no growth block the merge; the other rows are non-blocking._
@@ -9,7 +9,7 @@ _Duplicate keys (model unloadable) and no growth block the merge; the other rows
 | --- | ---: | ---: | :---: |
 | Duplicate `!!omap` keys | 0 | 0 | :white_check_mark: |
 | Reactions with no metabolites | 0 | 0 | :white_check_mark: |
-| Model / annotation-table inconsistencies | 0 | 0 | :white_check_mark: |
+| Model / annotation-table inconsistencies | [2](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/qc_annotation_consistency.csv) | +2 | :x: |
 | Growth (biomass producible) | 125 | 0 | :white_check_mark: |
 
 ### Model QC reports
@@ -23,17 +23,17 @@ _Duplicate keys (model unloadable) and no growth block the merge; the other rows
 | Unused metabolites | 0 | 0 | :white_check_mark: |
 | Unused genes | 0 | 0 | :white_check_mark: |
 | Malformed cross-references | 0 | 0 | :white_check_mark: |
-| Cross-refs inconsistent across compartments | [3](https://github.com/SysBioChalmers/Human-GEM/blob/worktree-matlab-to-python-workflows/data/testResults/qc_annotation_issues.csv) | 0 | :warning: |
+| Cross-refs inconsistent across compartments | [3](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/qc_annotation_issues.csv) | 0 | :warning: |
 
 ### MACAW and mass/charge balance
 
 | Check | Result | &Delta; vs `develop` | |
 | --- | ---: | ---: | :---: |
-| Reactions flagged by MACAW dead-end test | [2510](https://github.com/SysBioChalmers/Human-GEM/blob/worktree-matlab-to-python-workflows/data/testResults/macaw_results.csv) | 0 | :warning: |
-| Reactions flagged as MACAW duplicates | [377](https://github.com/SysBioChalmers/Human-GEM/blob/worktree-matlab-to-python-workflows/data/testResults/macaw_results.csv) | 0 | :warning: |
-| Mass-imbalanced reactions | [87](https://github.com/SysBioChalmers/Human-GEM/blob/worktree-matlab-to-python-workflows/data/testResults/balance_results.csv) | 0 | :warning: |
-| Charge-imbalanced reactions | [234](https://github.com/SysBioChalmers/Human-GEM/blob/worktree-matlab-to-python-workflows/data/testResults/balance_results.csv) | 0 | :warning: |
-| Structure vs formula/charge inconsistencies | [397](https://github.com/SysBioChalmers/Human-GEM/blob/worktree-matlab-to-python-workflows/data/testResults/qc_structure_consistency.csv) | 0 | :warning: |
+| Reactions flagged by MACAW dead-end test | [2511](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/macaw_results.csv) | +1 | :x: |
+| Reactions flagged as MACAW duplicates | [377](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/macaw_results.csv) | 0 | :warning: |
+| Mass-imbalanced reactions | [87](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/balance_results.csv) | 0 | :warning: |
+| Charge-imbalanced reactions | [234](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/balance_results.csv) | 0 | :warning: |
+| Structure vs formula/charge inconsistencies | [397](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/qc_structure_consistency.csv) | 0 | :warning: |
 
 ### Model file and metabolic tasks
 
diff --git a/data/testResults/qc_annotation_consistency.csv b/data/testResults/qc_annotation_consistency.csv
index 3d8d903e..01f3e494 100644
--- a/data/testResults/qc_annotation_consistency.csv
+++ b/data/testResults/qc_annotation_consistency.csv
@@ -1 +1,3 @@
 kind,id,issue
+reaction,MAR00483,deprecated identifier used
+reaction,MAR03838,deprecated identifier used

From 26dfd536b5a2e09a89eaef431ba087eb623081ff Mon Sep 17 00:00:00 2001
From: edkerk <7326655+edkerk@users.noreply.github.com>
Date: Sat, 18 Jul 2026 21:26:14 +0000
Subject: [PATCH 3/6] chore: update model QC results [skip ci]

---
 data/testResults/README.md           | 10 ++--
 data/testResults/model_qc_summary.md | 72 ++++++++++++++--------------
 2 files changed, 41 insertions(+), 41 deletions(-)

diff --git a/data/testResults/README.md b/data/testResults/README.md
index 6ed6d67d..53780ede 100644
--- a/data/testResults/README.md
+++ b/data/testResults/README.md
@@ -21,11 +21,11 @@ own files. The pull request in each row is the one whose run last wrote those fi
 
 | Result file(s) | Produced by | Last updated by |
 | --- | --- | --- |
-| `qc_duplicate_keys.csv`, `qc_empty_reactions.csv`, `qc_annotation_consistency.csv`, `qc_deprecation_completeness.csv`, `qc_metabolite_completeness.csv`, `qc_reaction_sanity.csv`, `qc_duplicate_reactions.csv`, `qc_unused_entities.csv`, `qc_growth_blockers.csv` | `qcModelChecks.py` | **PR #1061** (model QC checks) |
-| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1061** (model QC checks) |
-| `qc_status.tsv` (round-trip, YAML lint, metabolic tasks, growth) | `testYamlConversion.py`, `testMetabolicTasks.py`, `action-yamllint`, `qcModelChecks.py` (via `qcStatus.py`) | **PR #1061** (model QC checks) |
-| `macaw_results.csv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1061** (MACAW and balance) |
-| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1061** (MEMOTE) |
+| `qc_duplicate_keys.csv`, `qc_empty_reactions.csv`, `qc_annotation_consistency.csv`, `qc_deprecation_completeness.csv`, `qc_metabolite_completeness.csv`, `qc_reaction_sanity.csv`, `qc_duplicate_reactions.csv`, `qc_unused_entities.csv`, `qc_growth_blockers.csv` | `qcModelChecks.py` | **PR #1028** (model QC checks) |
+| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1028** (model QC checks) |
+| `qc_status.tsv` (round-trip, YAML lint, metabolic tasks, growth) | `testYamlConversion.py`, `testMetabolicTasks.py`, `action-yamllint`, `qcModelChecks.py` (via `qcStatus.py`) | **PR #1028** (model QC checks) |
+| `macaw_results.csv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1028** (MACAW and balance) |
+| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1028** (MEMOTE) |
 | `gene-essential.csv`, `gene-essential_summary.md` | `geneEssentiality.py` via `/run gene-essentiality` | **PR #1027** (gene essentiality) |
 
 ## 2. What each check means
diff --git a/data/testResults/model_qc_summary.md b/data/testResults/model_qc_summary.md
index fdac8f39..cb61b4ba 100644
--- a/data/testResults/model_qc_summary.md
+++ b/data/testResults/model_qc_summary.md
@@ -1,59 +1,59 @@
 ## Model quality report
 
-:warning: **6 pre-existing finding(s), no regressions vs `main`.** Non-blocking.
+:x: **2 regression(s) vs `develop`** (this pull request increased a finding count). Review the :x: rows.
 
-_Each check name links to its explanation in the [testResults README](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md)._
+_Each check name links to its explanation in the [testResults README](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md)._
 
 ### Model checks
 _Duplicate keys (model unloadable) and no growth block the merge; every other row is a non-blocking report._
 
-| Check | Result | &Delta; vs `main` | |
+| Check | Result | &Delta; vs `develop` | |
 | --- | ---: | ---: | :---: |
-| [Duplicate `!!omap` keys](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#duplicate-omap-keys) | 0 | new | :white_check_mark: |
-| [Growth (biomass producible)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#growth-biomass-producible) | 125 | new | :white_check_mark: |
-| [Reactions with no metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reactions-with-no-metabolites) | 0 | new | :white_check_mark: |
-| [Model / annotation-table inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#model--annotation-table-inconsistencies) | 0 | new | :white_check_mark: |
-| [Removed reactions or metabolites not deprecated](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#removed-reactions-or-metabolites-not-deprecated) | 0 | new | :white_check_mark: |
-| [Metabolites missing formula](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#metabolites-missing-formula) | 0 | new | :white_check_mark: |
-| [Metabolites missing charge](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#metabolites-missing-charge) | 0 | new | :white_check_mark: |
-| [Reaction bound / GPR issues](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reaction-bound--gpr-issues) | 0 | new | :white_check_mark: |
-| [Exact-duplicate reaction groups](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#exact-duplicate-reaction-groups) | 0 | new | :white_check_mark: |
-| [Unused metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#unused-metabolites) | 0 | new | :white_check_mark: |
-| [Unused genes](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#unused-genes) | 0 | new | :white_check_mark: |
-| [Malformed cross-references](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#malformed-cross-references) | 0 | new | :white_check_mark: |
-| [Cross-refs inconsistent across compartments](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#cross-refs-inconsistent-across-compartments) | [3](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/qc_annotation_issues.csv) | new | :warning: |
+| [Duplicate `!!omap` keys](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#duplicate-omap-keys) | 0 | 0 | :white_check_mark: |
+| [Growth (biomass producible)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#growth-biomass-producible) | 125 | 0 | :white_check_mark: |
+| [Reactions with no metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#reactions-with-no-metabolites) | 0 | 0 | :white_check_mark: |
+| [Model / annotation-table inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#model--annotation-table-inconsistencies) | [2](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/qc_annotation_consistency.csv) | +2 | :x: |
+| [Removed reactions or metabolites not deprecated](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#removed-reactions-or-metabolites-not-deprecated) | 0 | 0 | :white_check_mark: |
+| [Metabolites missing formula](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#metabolites-missing-formula) | 0 | 0 | :white_check_mark: |
+| [Metabolites missing charge](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#metabolites-missing-charge) | 0 | 0 | :white_check_mark: |
+| [Reaction bound / GPR issues](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#reaction-bound--gpr-issues) | 0 | 0 | :white_check_mark: |
+| [Exact-duplicate reaction groups](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#exact-duplicate-reaction-groups) | 0 | 0 | :white_check_mark: |
+| [Unused metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#unused-metabolites) | 0 | 0 | :white_check_mark: |
+| [Unused genes](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#unused-genes) | 0 | 0 | :white_check_mark: |
+| [Malformed cross-references](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#malformed-cross-references) | 0 | 0 | :white_check_mark: |
+| [Cross-refs inconsistent across compartments](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#cross-refs-inconsistent-across-compartments) | [3](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/qc_annotation_issues.csv) | 0 | :warning: |
 
 ### MACAW and mass/charge balance
 
-| Check | Result | &Delta; vs `main` | |
+| Check | Result | &Delta; vs `develop` | |
 | --- | ---: | ---: | :---: |
-| [Reactions flagged by MACAW dead-end test](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reactions-flagged-by-macaw-dead-end-test) | [2510](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/macaw_results.csv) | -703 | :warning: |
-| [Reactions flagged as MACAW duplicates](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reactions-flagged-as-macaw-duplicates) | [377](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/macaw_results.csv) | -2 | :warning: |
-| [Mass-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#mass-imbalanced-reactions) | [87](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/balance_results.csv) | new | :warning: |
-| [Charge-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#charge-imbalanced-reactions) | [234](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/balance_results.csv) | new | :warning: |
-| [Structure vs formula/charge inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#structure-vs-formulacharge-inconsistencies) | [397](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/qc_structure_consistency.csv) | new | :warning: |
+| [Reactions flagged by MACAW dead-end test](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#reactions-flagged-by-macaw-dead-end-test) | [2511](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/macaw_results.csv) | +1 | :x: |
+| [Reactions flagged as MACAW duplicates](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#reactions-flagged-as-macaw-duplicates) | [377](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/macaw_results.csv) | 0 | :warning: |
+| [Mass-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#mass-imbalanced-reactions) | [87](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/balance_results.csv) | 0 | :warning: |
+| [Charge-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#charge-imbalanced-reactions) | [234](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/balance_results.csv) | 0 | :warning: |
+| [Structure vs formula/charge inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#structure-vs-formulacharge-inconsistencies) | [397](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/qc_structure_consistency.csv) | 0 | :warning: |
 
 ### Model file and metabolic tasks
 
 | Check | Result | |
 | --- | ---: | :---: |
-| [YAML round-trip (cobrapy)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#yaml-round-trip-cobrapy) | pass | :white_check_mark: |
-| [YAML round-trip (RAVEN)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#yaml-round-trip-raven) | pass | :white_check_mark: |
-| [YAML lint](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#yaml-lint) | pass | :white_check_mark: |
-| [Essential metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#essential-metabolic-tasks) | 57 passed | :white_check_mark: |
-| [Verification metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#verification-metabolic-tasks) | 21 passed | :white_check_mark: |
+| [YAML round-trip (cobrapy)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#yaml-round-trip-cobrapy) | pass | :white_check_mark: |
+| [YAML round-trip (RAVEN)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#yaml-round-trip-raven) | pass | :white_check_mark: |
+| [YAML lint](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#yaml-lint) | pass | :white_check_mark: |
+| [Essential metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#essential-metabolic-tasks) | 57 passed | :white_check_mark: |
+| [Verification metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#verification-metabolic-tasks) | 21 passed | :white_check_mark: |
 
-### [MEMOTE](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#memote)
+### [MEMOTE](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#memote)
 
-**Total score: 63.2%** (core subset) &nbsp;
+**Total score: 63.2%** (core subset) &nbsp; 0
 
 | Section | Score | &Delta; vs base |
 | --- | ---: | ---: |
-| consistency | 42.4% |  |
-| annotation_met | 73.0% |  |
-| annotation_rxn | 72.7% |  |
-| annotation_gene | 46.7% |  |
-| annotation_sbo | 81.7% |  |
+| consistency | 42.4% | 0 |
+| annotation_met | 73.0% | 0 |
+| annotation_rxn | 72.7% | 0 |
+| annotation_gene | 46.7% | 0 |
+| annotation_sbo | 81.7% | 0 |
 
 <details><summary>Per-test scores</summary>
 
@@ -89,11 +89,11 @@ _Duplicate keys (model unloadable) and no growth block the merge; every other ro
 
 </details>
 
-**Full suite: 64.2%** &nbsp;  &middot; _from the last_ `/run memote`.
+**Full suite: 64.2%** &nbsp; 0 &middot; _from the last_ `/run memote`.
 
 _The score above is the fast core subset. Comment_ `/run memote` _to run the full suite on this pull request; the score updates here when it finishes._
 
-### [Gene essentiality (Hart 2015)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#gene-essentiality-hart-2015)
+### [Gene essentiality (Hart 2015)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#gene-essentiality-hart-2015)
 
 _Not run automatically (it takes hours). Comment_ `/run gene-essentiality` _to run it on this pull request; the result posts as its own comment._
 

From 3d6583b93413ef334d4737f3ff1838cd5356425c Mon Sep 17 00:00:00 2001
From: Eduard Kerkhoven <eduardk@chalmers.se>
Date: Sun, 19 Jul 2026 00:22:28 +0200
Subject: [PATCH 4/6] fix: remove orphaned mitochondrial DHAP node after GPD2
 recoupling

Removing the FAD-linked MAR00449 left MAM01690m (mitochondrial DHAP)
without a producer, since the restored ubiquinone-linked GPD2 (MAR00483)
releases cytosolic DHAP. The metabolite and its only remaining reaction,
the export transport MAR08111, are a MACAW dead-end and are removed and
moved to the deprecated identifier lists.

Drop the stale MAR00483 and MAR03838 rows from deprecatedReactions.tsv,
as those identifiers are active reactions again after this PR.
---
 .../deprecatedMetabolites.tsv                  |  1 +
 .../deprecatedReactions.tsv                    |  5 ++---
 model/Human-GEM.yml                            | 18 ------------------
 model/metabolites.tsv                          |  1 -
 model/reactions.tsv                            |  1 -
 5 files changed, 3 insertions(+), 23 deletions(-)

diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv
index 66f1b180..b3ad2a38 100644
--- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv
+++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv
@@ -2272,3 +2272,4 @@ MAM00208c	MAM00208		C16832							M00208	MNXM21289	m00208c	m00208c
 MAM00209c	MAM00209		C16237							M00209	MNXM96070	m00209c	m00209c
 MAM00210c	MAM00210		C16236							M00210	MNXM4090	m00210c	m00210c
 MAM01622x	MAM01622	b2coa	C00877		CHEBI:15473	5280381			HC00572	b2coa	MNXM214	m01622p	m01622p
+MAM01690m	MAM01690	dhap	C00111		CHEBI:16108	668			HC00109	dhap	MNXM77	m01690m	m01690m
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
index bfb897b4..349f2b01 100644
--- a/data/deprecatedIdentifiers/deprecatedReactions.tsv
+++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -108,13 +108,11 @@ MAR03751	R02660		R02660M	r0560		r0560		HMR_3751	RCR14421		0			HMR_3751
 MAR03783	R03172		R03172M	r0603		r0603	MNXR108000	HMR_3783	RCR14424		0			HMR_3783
 MAR04242	R02487		R02487M	r0541		r0541	MNXR100293	HMR_4242	RCR14356		0		RHEA:30847	HMR_4242
 MAR03769	R04095		R04095M	r0655		r0655	MNXR95318	HMR_3769	RCR14423		0			HMR_3769
-MAR03838				r1453				HMR_3838	RCR14286		0			HMR_3838
 MAR02366		r1446				r1446					0			r1446
 MAR02367		r1447				r1447					0			r1447
 MAR02370		r1449				r1449					0			r1449
 MAR02372		r1450				r1450					0			r1450
 MAR02373		r1451				r1451					0			r1451
-MAR00483	R00849			r0205		r0205	MNXR106713	HMR_0483	RCR21050		0		RHEA:18977	HMR_0483
 MAR08743	R00408	SUCD1m				SUCD1m	MNXR99636	HMR_8743	RCR11674		0		RHEA:30343	HMR_8743
 MAR05294	R00362		R00362C	r1109		r1109	MNXR96731	HMR_5294	RCR11670		0	RHEA:10761	RHEA:10760	HMR_5294
 MAR11421		CITL				CITL	MNXR96731				0	RHEA:10761	RHEA:10760	CITL
@@ -404,4 +402,5 @@ MAR07854		DNDPt7m				DNDPt7m	MNXR97175	HMR_7854	RCR20122		0			HMR_7854
 
 MAR08611	R10507	PROD2m		r1453		PROD2m	MNXR103187	HMR_8611;HMR_3838	RCR11294;RCR14286		0			HMR_8611;HMR_3838;MAR03838
 MAR00449	R00848;R00849			r0205	R-HSA-188467	GLYC3PFADm;r0205	MNXR99875;MNXR106713	HMR_0449;HMR_0483	RCR12494;RCR21050		0		RHEA:31283;RHEA:18977	HMR_0449;HMR_0483
-MAR01169	R00849;R00848	G3PD2m	R00848C	r0205		G3PD2m;r0205;HMR_0482	MNXR99878;MNXR106713;MNXR192664	HMR_0483;HMR_0482	RCR21050;RCR14578		0		RHEA:18977	G3PD2m;HMR_0483;HMR_0482;MAR00482;MAR00483
\ No newline at end of file
+MAR01169	R00849;R00848	G3PD2m	R00848C	r0205		G3PD2m;r0205;HMR_0482	MNXR99878;MNXR106713;MNXR192664	HMR_0483;HMR_0482	RCR21050;RCR14578		0		RHEA:18977	G3PD2m;HMR_0483;HMR_0482;MAR00482;MAR00483
+MAR08111		DHAPtm				DHAPtc	MNXR97366				0			DHAPtc
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
index bbcd3adc..5727b491 100644
--- a/model/Human-GEM.yml
+++ b/model/Human-GEM.yml
@@ -19996,13 +19996,6 @@
       - formula: "C3H5O6P"
       - charge: -2
       - metFrom: "HMRdatabase"
-    - !!omap
-      - id: "MAM01690m"
-      - name: "DHAP"
-      - compartment: "m"
-      - formula: "C3H5O6P"
-      - charge: -2
-      - metFrom: "HMRdatabase"
     - !!omap
       - id: "MAM01690x"
       - name: "DHAP"
@@ -205583,17 +205576,6 @@
       - references: "PMID:16816105;PMID:17403938"
       - subsystem: "Transport reactions"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR08111"
-      - name: "Transport of Dihydroxyacetone Phosphate into Cytosol"
-      - metabolites: !!omap
-          - MAM01690c: 1
-          - MAM01690m: -1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - rxnFrom: "Recon3D"
-      - subsystem: "Transport reactions"
-      - confidence_score: 0
     - !!omap
       - id: "MAR08204"
       - name: "pyrophasphatase (dephospho-CoA, extracellular)"
diff --git a/model/metabolites.tsv b/model/metabolites.tsv
index be4644ca..4b201454 100644
--- a/model/metabolites.tsv
+++ b/model/metabolites.tsv
@@ -2827,7 +2827,6 @@ MAM01689l	MAM01689	crvnc	C06429	HMDB0002183	CHEBI:77016	445580	LMFA01030185	CE03
 MAM01689r	MAM01689	crvnc	C06429	HMDB0002183	CHEBI:77016	445580	LMFA01030185	CE0328		crvnc	MNXM7161	CC/C=C\C/C=C\C/C=C\C/C=C\C/C=C\C/C=C\CCC(=O)[O-]	InChI=1S/C22H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22(23)24/h3-4,6-7,9-10,12-13,15-16,18-19H,2,5,8,11,14,17,20-21H2,1H3,(H,23,24)/p-1/b4-3-,7-6-,10-9-,13-12-,16-15-,19-18-	cpd03852	m01689r	m01689r
 MAM01689e	MAM01689	crvnc	C06429	HMDB0002183	CHEBI:77016	445580	LMFA01030185	CE0328		crvnc	MNXM7161	CC/C=C\C/C=C\C/C=C\C/C=C\C/C=C\C/C=C\CCC(=O)[O-]	InChI=1S/C22H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22(23)24/h3-4,6-7,9-10,12-13,15-16,18-19H,2,5,8,11,14,17,20-21H2,1H3,(H,23,24)/p-1/b4-3-,7-6-,10-9-,13-12-,16-15-,19-18-	cpd03852	m01689s	m01689s
 MAM01690c	MAM01690	dhap	C00111	HMDB0001473	CHEBI:16108	668			HC00109	dhap	MNXM77	O=C(CO)COP(=O)([O-])[O-]	InChI=1S/C3H7O6P/c4-1-3(5)2-9-10(6,7)8/h4H,1-2H2,(H2,6,7,8)/p-2	cpd00095	m01690c	m01690c
-MAM01690m	MAM01690	dhap	C00111	HMDB0001473	CHEBI:16108	668			HC00109	dhap	MNXM77	O=C(CO)COP(=O)([O-])[O-]	InChI=1S/C3H7O6P/c4-1-3(5)2-9-10(6,7)8/h4H,1-2H2,(H2,6,7,8)/p-2	cpd00095	m01690m	m01690m
 MAM01690x	MAM01690	dhap	C00111	HMDB0001473	CHEBI:16108	668			HC00109	dhap	MNXM77	O=C(CO)COP(=O)([O-])[O-]	InChI=1S/C3H7O6P/c4-1-3(5)2-9-10(6,7)8/h4H,1-2H2,(H2,6,7,8)/p-2	cpd00095	m01690p	m01690p
 MAM01690e	MAM01690	dhap	C00111	HMDB0001473	CHEBI:16108	668			HC00109	dhap	MNXM77	O=C(CO)COP(=O)([O-])[O-]	InChI=1S/C3H7O6P/c4-1-3(5)2-9-10(6,7)8/h4H,1-2H2,(H2,6,7,8)/p-2	cpd00095	m01690s	m01690s
 MAM01691c	MAM01691		C11149		CHEBI:28240		LMFA01090070			M01691	MNXM5126	O=C([O-])C(Cl)Cl	InChI=1S/C2H2Cl2O2/c3-1(4)2(5)6/h1H,(H,5,6)/p-1	cpd08027	m01691c	m01691c
diff --git a/model/reactions.tsv b/model/reactions.tsv
index e144c0a1..61427fe3 100644
--- a/model/reactions.tsv
+++ b/model/reactions.tsv
@@ -9364,7 +9364,6 @@ MAR07813		BIDGLCURr				BIDGLCURr	MNXR154864				0			BIDGLCURr
 MAR07817	R02467	CYSAMOe				CYSAMOe	MNXR96988				0	RHEA:14410	RHEA:14409	CYSAMOe
 MAR07819		Coqe				Coqe	MNXR97066				0			Coqe
 MAR07821		DATPtm_cho				DATPtm	MNXR97176				0			DATPtm
-MAR08111		DHAPtm				DHAPtc	MNXR97366				0			DHAPtc
 MAR08204		DPCOAPPe				DPCOAPPe	MNXR97763				0			DPCOAPPe
 MAR08218	R01457	DSREDUCr				DSREDUCr	MNXR97801				0	RHEA:36391		DSREDUCr
 MAR08274	R02094	DTMPKm				DTMPKm	MNXR97804				0	RHEA:13518	RHEA:13517	DTMPKm

From 72a85239812635eaef78d27c97e8ba13a222f2c7 Mon Sep 17 00:00:00 2001
From: edkerk <7326655+edkerk@users.noreply.github.com>
Date: Sat, 18 Jul 2026 22:40:53 +0000
Subject: [PATCH 5/6] chore: update model QC results [skip ci]

---
 data/testResults/macaw_results.csv             | 1 -
 data/testResults/model_qc_summary.md           | 6 +++---
 data/testResults/qc_annotation_consistency.csv | 2 --
 3 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/data/testResults/macaw_results.csv b/data/testResults/macaw_results.csv
index 06a044a4..72c6151d 100644
--- a/data/testResults/macaw_results.csv
+++ b/data/testResults/macaw_results.csv
@@ -9364,7 +9364,6 @@ MAR07813,MAM01398r + MAM03109r --> MAM01397r + MAM03106r,ok,ok,ok,ok,N/A
 MAR07817,MAM01627e + MAM02630e --> MAM02039e + MAM02157e,ok,ok,ok,ok,N/A
 MAR07819,MAM03103e <=> MAM03103c,ok,ok,ok,ok,N/A
 MAR07821,MAM01642c --> MAM01642m,ok,ok,ok,ok,N/A
-MAR08111,MAM01690m --> MAM01690c,MAM01690m,ok,ok,ok,N/A
 MAR08204,MAM01674e + MAM02040e --> MAM01334e + 2 MAM02039e + MAM02741e,ok,ok,ok,ok,N/A
 MAR08218,MAM01675r + MAM02039r + MAM02555r --> MAM01450r + MAM02554r,ok,ok,ok,ok,N/A
 MAR08274,MAM01371m + MAM01752m --> MAM01285m + MAM01747m,ok,ok,ok,ok,N/A
diff --git a/data/testResults/model_qc_summary.md b/data/testResults/model_qc_summary.md
index cb61b4ba..e0a932e3 100644
--- a/data/testResults/model_qc_summary.md
+++ b/data/testResults/model_qc_summary.md
@@ -1,6 +1,6 @@
 ## Model quality report
 
-:x: **2 regression(s) vs `develop`** (this pull request increased a finding count). Review the :x: rows.
+:warning: **6 pre-existing finding(s), no regressions vs `develop`.** Non-blocking.
 
 _Each check name links to its explanation in the [testResults README](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md)._
 
@@ -12,7 +12,7 @@ _Duplicate keys (model unloadable) and no growth block the merge; every other ro
 | [Duplicate `!!omap` keys](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#duplicate-omap-keys) | 0 | 0 | :white_check_mark: |
 | [Growth (biomass producible)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#growth-biomass-producible) | 125 | 0 | :white_check_mark: |
 | [Reactions with no metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#reactions-with-no-metabolites) | 0 | 0 | :white_check_mark: |
-| [Model / annotation-table inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#model--annotation-table-inconsistencies) | [2](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/qc_annotation_consistency.csv) | +2 | :x: |
+| [Model / annotation-table inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#model--annotation-table-inconsistencies) | 0 | 0 | :white_check_mark: |
 | [Removed reactions or metabolites not deprecated](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#removed-reactions-or-metabolites-not-deprecated) | 0 | 0 | :white_check_mark: |
 | [Metabolites missing formula](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#metabolites-missing-formula) | 0 | 0 | :white_check_mark: |
 | [Metabolites missing charge](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#metabolites-missing-charge) | 0 | 0 | :white_check_mark: |
@@ -27,7 +27,7 @@ _Duplicate keys (model unloadable) and no growth block the merge; every other ro
 
 | Check | Result | &Delta; vs `develop` | |
 | --- | ---: | ---: | :---: |
-| [Reactions flagged by MACAW dead-end test](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#reactions-flagged-by-macaw-dead-end-test) | [2511](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/macaw_results.csv) | +1 | :x: |
+| [Reactions flagged by MACAW dead-end test](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#reactions-flagged-by-macaw-dead-end-test) | [2510](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/macaw_results.csv) | 0 | :warning: |
 | [Reactions flagged as MACAW duplicates](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#reactions-flagged-as-macaw-duplicates) | [377](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/macaw_results.csv) | 0 | :warning: |
 | [Mass-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#mass-imbalanced-reactions) | [87](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/balance_results.csv) | 0 | :warning: |
 | [Charge-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#charge-imbalanced-reactions) | [234](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/balance_results.csv) | 0 | :warning: |
diff --git a/data/testResults/qc_annotation_consistency.csv b/data/testResults/qc_annotation_consistency.csv
index 01f3e494..3d8d903e 100644
--- a/data/testResults/qc_annotation_consistency.csv
+++ b/data/testResults/qc_annotation_consistency.csv
@@ -1,3 +1 @@
 kind,id,issue
-reaction,MAR00483,deprecated identifier used
-reaction,MAR03838,deprecated identifier used

From a819744836b60bd03724f422ac87b721c7ba5741 Mon Sep 17 00:00:00 2001
From: edkerk <7326655+edkerk@users.noreply.github.com>
Date: Sun, 19 Jul 2026 11:49:55 +0200
Subject: [PATCH 6/6] chore: add gene essentiality test result [skip ci]

---
 data/testResults/README.md                 |   2 +-
 data/testResults/gene-essential.csv        | 138 ++++++++++-----------
 data/testResults/gene-essential_summary.md |  12 +-
 3 files changed, 76 insertions(+), 76 deletions(-)

diff --git a/data/testResults/README.md b/data/testResults/README.md
index 53780ede..df7bdd85 100644
--- a/data/testResults/README.md
+++ b/data/testResults/README.md
@@ -26,7 +26,7 @@ own files. The pull request in each row is the one whose run last wrote those fi
 | `qc_status.tsv` (round-trip, YAML lint, metabolic tasks, growth) | `testYamlConversion.py`, `testMetabolicTasks.py`, `action-yamllint`, `qcModelChecks.py` (via `qcStatus.py`) | **PR #1028** (model QC checks) |
 | `macaw_results.csv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1028** (MACAW and balance) |
 | `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1028** (MEMOTE) |
-| `gene-essential.csv`, `gene-essential_summary.md` | `geneEssentiality.py` via `/run gene-essentiality` | **PR #1027** (gene essentiality) |
+| `gene-essential.csv`, `gene-essential_summary.md` | `geneEssentiality.py` via `/run gene-essentiality` | **PR #1028** (gene essentiality) |
 
 ## 2. What each check means
 
diff --git a/data/testResults/gene-essential.csv b/data/testResults/gene-essential.csv
index 5e18d532..e38a1da0 100644
--- a/data/testResults/gene-essential.csv
+++ b/data/testResults/gene-essential.csv
@@ -25,7 +25,7 @@ ENSG00000005187,ACSM3,TN,TN,TN,TN,TN
 ENSG00000005339,CREBBP,TN,TN,FN,TN,TN
 ENSG00000005381,MPO,TN,TN,TN,TN,TN
 ENSG00000005421,PON1,TN,TN,TN,TN,TN
-ENSG00000005469,CROT,TN,TN,TN,TN,FP
+ENSG00000005469,CROT,TN,FP,TN,TN,FP
 ENSG00000005471,ABCB4,TN,TN,TN,TN,TN
 ENSG00000005810,MYCBP2,TN,TN,TN,TN,TN
 ENSG00000005882,PDK2,TN,TN,TN,TN,FN
@@ -134,10 +134,10 @@ ENSG00000047230,CTPS2,TN,TN,TN,TN,TN
 ENSG00000047249,ATP6V1H,FN,TN,FN,FN,FN
 ENSG00000047315,POLR2B,TP,TP,TP,TP,TP
 ENSG00000047410,TPR,TP,TP,TP,TP,FP
-ENSG00000047457,CP,TN,TN,TN,TN,TN
+ENSG00000047457,CP,FP,TN,TN,TN,TN
 ENSG00000048028,USP28,TN,TN,TN,TN,TN
 ENSG00000048392,RRM2B,FP,FP,FP,FP,FP
-ENSG00000049239,H6PD,FP,FP,FP,FP,TN
+ENSG00000049239,H6PD,FP,FP,FP,TN,TN
 ENSG00000049759,NEDD4L,TN,TN,TN,TN,TN
 ENSG00000049860,HEXB,TN,TN,TN,TN,TN
 ENSG00000050438,SLC4A8,TN,TN,TN,TN,TN
@@ -163,7 +163,7 @@ ENSG00000059378,PARP12,TN,TN,TN,TN,TN
 ENSG00000059573,ALDH18A1,FN,TN,TN,FN,TN
 ENSG00000059804,SLC2A3,.,.,FN,TN,.
 ENSG00000060642,PIGV,FN,FN,TN,FN,TN
-ENSG00000060762,MPC1,TN,TN,TN,FP,TN
+ENSG00000060762,MPC1,TN,TN,TN,TN,TN
 ENSG00000060971,ACAA1,FP,FP,FP,FP,TP
 ENSG00000060982,BCAT1,TN,TN,TN,TN,FN
 ENSG00000061918,GUCY1B1,TN,TN,TN,TN,TN
@@ -191,7 +191,7 @@ ENSG00000065911,MTHFD2,TN,TN,TN,FN,TN
 ENSG00000065923,SLC9A7,TN,TN,TN,TN,TN
 ENSG00000065989,PDE4A,TN,TN,TN,TN,TN
 ENSG00000066230,SLC9A3,TN,TN,TN,TN,TN
-ENSG00000066322,ELOVL1,FP,FP,FP,FP,FP
+ENSG00000066322,ELOVL1,FP,TN,FP,FP,FP
 ENSG00000066379,POLR1H,TP,TP,TP,TP,TP
 ENSG00000066651,TRMT11,TN,TN,TN,TN,TN
 ENSG00000066813,ACSM2B,TN,TN,FN,TN,TN
@@ -241,14 +241,14 @@ ENSG00000071794,HLTF,TN,TN,TN,TN,TN
 ENSG00000071967,CYBRD1,TN,FN,TN,TN,TN
 ENSG00000072041,SLC6A15,TN,TN,TN,TN,TN
 ENSG00000072042,RDH11,TN,TN,TN,TN,TN
-ENSG00000072210,ALDH3A2,TN,TN,TN,TN,TN
+ENSG00000072210,ALDH3A2,TN,FP,TN,TN,FP
 ENSG00000072274,TFRC,FN,TN,FN,TN,TN
 ENSG00000072401,UBE2D1,TN,TN,TN,TN,TN
 ENSG00000072506,HSD17B10,TP,TP,TP,TP,FP
 ENSG00000072609,CHFR,TN,TN,TN,TN,TN
 ENSG00000072657,TRHDE,TN,TN,TN,TN,TN
 ENSG00000072682,P4HA2,TN,FN,TN,TN,TN
-ENSG00000072778,ACADVL,FP,TN,FP,TN,TN
+ENSG00000072778,ACADVL,TN,TN,TN,FP,FP
 ENSG00000073060,SCARB1,FP,FP,FP,FP,FP
 ENSG00000073417,PDE8A,TN,TN,TN,TN,TN
 ENSG00000073578,SDHA,TP,FP,TP,FP,TP
@@ -311,7 +311,7 @@ ENSG00000081800,SLC13A1,TN,TN,TN,TN,TN
 ENSG00000081923,ATP8B1,TN,TN,TN,TN,TN
 ENSG00000082212,ME2,TN,TN,TN,TN,TN
 ENSG00000082996,RNF13,.,.,TN,TN,.
-ENSG00000083123,BCKDHB,TN,TN,FP,FP,TN
+ENSG00000083123,BCKDHB,TN,FP,TN,TN,FP
 ENSG00000083168,KAT6A,TN,TN,TN,TN,TN
 ENSG00000083223,TUT7,TN,TN,TN,TN,TN
 ENSG00000083444,PLOD1,TN,TN,TN,TN,FN
@@ -428,7 +428,7 @@ ENSG00000100023,PPIL2,FN,FN,FN,FN,FN
 ENSG00000100024,UPB1,TN,TN,TN,TN,TN
 ENSG00000100031,GGT1,.,.,.,.,.
 ENSG00000100033,PRODH,TN,TN,TN,TN,TN
-ENSG00000100075,SLC25A1,TN,TN,TN,TN,TN
+ENSG00000100075,SLC25A1,TN,TN,TN,FP,TN
 ENSG00000100077,GRK3,TN,TN,TN,TN,TN
 ENSG00000100078,PLA2G3,TN,TN,TN,TN,TN
 ENSG00000100092,SH3BP1,TN,TN,TN,TN,TN
@@ -448,7 +448,7 @@ ENSG00000100299,ARSA,TN,TN,TN,TN,TN
 ENSG00000100344,PNPLA3,TN,TN,TN,TN,TN
 ENSG00000100348,TXN2,FN,TN,FN,FN,FN
 ENSG00000100354,TNRC6B,TN,TN,TN,TN,TN
-ENSG00000100372,SLC25A17,TN,TN,TN,TN,FP
+ENSG00000100372,SLC25A17,TN,FP,FP,TN,FP
 ENSG00000100393,EP300,FN,TN,TN,TN,TN
 ENSG00000100412,ACO2,FN,FN,FN,FN,TN
 ENSG00000100413,POLR3H,TP,TP,TP,TP,TP
@@ -514,7 +514,7 @@ ENSG00000102032,RENBP,TN,TN,TN,TN,TN
 ENSG00000102043,MTMR8,TN,TN,TN,TN,TN
 ENSG00000102078,SLC25A14,TN,TN,TN,TN,TN
 ENSG00000102100,SLC35A2,TN,TN,TN,TN,TN
-ENSG00000102144,PGK1,TP,FN,TP,TP,FN
+ENSG00000102144,PGK1,TP,FN,TP,FN,FN
 ENSG00000102172,SMS,TN,TN,TN,TN,TN
 ENSG00000102226,USP11,TN,TN,TN,TN,TN
 ENSG00000102230,PCYT1B,TN,TN,TN,TN,TN
@@ -525,7 +525,7 @@ ENSG00000102393,GLA,TN,TN,TN,TN,TN
 ENSG00000102452,NALCN,TN,TN,TN,TN,TN
 ENSG00000102575,ACP5,TN,TN,TN,TN,TN
 ENSG00000102699,PARP4,TN,TN,TN,TN,TN
-ENSG00000102743,SLC25A15,FN,TN,FN,TP,TN
+ENSG00000102743,SLC25A15,FN,TN,FN,FN,FP
 ENSG00000102780,DGKH,TN,TN,TN,TN,TN
 ENSG00000102794,ACOD1,FN,TN,FN,FN,TN
 ENSG00000102858,MGRN1,TN,TN,TN,TN,TN
@@ -567,7 +567,7 @@ ENSG00000104044,OCA2,TN,TN,TN,TN,TN
 ENSG00000104055,TGM5,TN,TN,TN,TN,TN
 ENSG00000104219,ZDHHC2,TN,TN,TN,TN,FN
 ENSG00000104267,CA2,TN,TN,TN,TN,TN
-ENSG00000104325,DECR1,FP,TN,FP,FP,TN
+ENSG00000104325,DECR1,FP,FP,FP,FP,FP
 ENSG00000104331,BPNT2,TN,TN,TN,TN,TN
 ENSG00000104343,UBE2W,.,.,TN,TN,.
 ENSG00000104517,UBR5,TN,TN,TN,TN,TN
@@ -581,26 +581,26 @@ ENSG00000104763,ASAH1,TN,TN,TN,TN,TN
 ENSG00000104774,MAN2B1,TN,TN,TN,TN,TN
 ENSG00000104808,DHDH,TN,TN,TN,TN,TN
 ENSG00000104812,GYS1,TN,TN,TN,TN,TN
-ENSG00000104823,ECH1,FP,TN,FP,FP,TN
+ENSG00000104823,ECH1,FP,FP,FP,FP,TN
 ENSG00000104879,CKM,TN,TN,FN,TN,TN
 ENSG00000104885,DOT1L,FN,FN,TN,TN,FN
 ENSG00000104888,SLC17A7,TN,FN,FP,TN,TN
 ENSG00000104907,TRMT1,FN,FN,TN,TN,TN
 ENSG00000104951,IL4I1,TN,TN,TN,TN,TN
 ENSG00000105143,SLC1A6,TN,TN,TN,TN,TN
-ENSG00000105220,GPI,TP,TN,TP,TP,TN
+ENSG00000105220,GPI,TP,TN,TP,FN,TN
 ENSG00000105254,TBCB,FN,TN,TN,TN,FN
 ENSG00000105258,POLR2I,TP,TP,TP,TP,TP
 ENSG00000105281,SLC1A5,TN,TN,TN,TN,TN
 ENSG00000105355,PLIN3,TN,TN,TN,TN,TN
-ENSG00000105379,ETFB,TN,TN,TN,TN,TN
+ENSG00000105379,ETFB,FP,FP,FP,FP,FP
 ENSG00000105398,SULT2A1,TN,TN,TN,TN,TN
 ENSG00000105409,ATP1A3,TN,TN,TN,TN,TN
 ENSG00000105499,PLA2G4C,TN,TN,TN,TN,TN
 ENSG00000105509,HAS1,TN,TN,TN,TN,TN
 ENSG00000105516,DBP,TN,TN,TN,TN,TN
 ENSG00000105520,PLPPR2,.,.,.,.,.
-ENSG00000105552,BCAT2,TN,TN,FP,FP,TN
+ENSG00000105552,BCAT2,TN,FP,TN,TN,FP
 ENSG00000105607,GCDH,TN,TN,TN,TN,TN
 ENSG00000105641,SLC5A5,TN,TN,TN,TN,TN
 ENSG00000105647,PIK3R2,FN,TN,TN,TN,TN
@@ -677,7 +677,7 @@ ENSG00000108846,ABCC3,TN,TN,TN,TN,TN
 ENSG00000108854,SMURF2,TN,TN,FN,TN,TN
 ENSG00000108932,SLC16A6,TN,TN,TN,TN,TN
 ENSG00000109065,NAT9,TN,TN,TN,TN,TN
-ENSG00000109107,ALDOC,TN,TN,FP,FP,TN
+ENSG00000109107,ALDOC,TN,TN,FP,TN,TN
 ENSG00000109181,UGT2B10,.,.,.,.,.
 ENSG00000109189,USP46,TN,TN,TN,TN,TN
 ENSG00000109193,SULT1E1,TN,TN,TN,TN,TN
@@ -700,7 +700,7 @@ ENSG00000109956,B3GAT1,TN,TN,TN,TN,TN
 ENSG00000110013,SIAE,TN,TN,TN,TN,TN
 ENSG00000110066,KMT5B,FN,FN,TN,TN,FN
 ENSG00000110080,ST3GAL4,TN,TN,TN,TN,TN
-ENSG00000110090,CPT1A,FP,TN,FP,FP,TN
+ENSG00000110090,CPT1A,FP,FP,FP,FP,TN
 ENSG00000110195,FOLR1,TN,TN,TN,TN,TN
 ENSG00000110203,FOLR3,TN,TN,TN,TN,TN
 ENSG00000110245,APOC3,TN,TN,TN,TN,TN
@@ -747,7 +747,7 @@ ENSG00000111684,LPCAT3,TN,TN,TN,TN,TN
 ENSG00000111696,NT5DC3,TN,TN,TN,TN,TN
 ENSG00000111700,SLCO1B3,TN,TN,TN,TN,TN
 ENSG00000111713,GYS2,TN,TN,TN,TN,TN
-ENSG00000111716,LDHB,.,.,TN,TN,.
+ENSG00000111716,LDHB,.,.,TN,TN,P
 ENSG00000111726,CMAS,TN,TN,TN,TN,TN
 ENSG00000111728,ST8SIA1,TN,TN,TN,TN,TN
 ENSG00000111732,AICDA,TN,TN,TN,TN,TN
@@ -779,7 +779,7 @@ ENSG00000112759,SLC29A1,TN,TN,TN,TN,TN
 ENSG00000112874,NUDT12,TN,TN,TN,TN,TN
 ENSG00000112893,MAN2A1,TN,TN,TN,TN,TN
 ENSG00000112941,TENT4A,TN,TN,TN,TN,TN
-ENSG00000112972,HMGCS1,TP,TP,TP,FN,TN
+ENSG00000112972,HMGCS1,FN,TP,TP,FN,FP
 ENSG00000112992,NNT,TN,TN,TN,TN,TN
 ENSG00000113013,HSPA9,FN,FN,FN,FN,FN
 ENSG00000113073,SLC4A9,TN,FN,TN,TN,TN
@@ -877,14 +877,14 @@ ENSG00000116459,ATP5PB,TP,TP,TP,TP,FP
 ENSG00000116514,RNF19B,TN,TN,TN,TN,TN
 ENSG00000116539,ASH1L,TN,TN,TN,TN,TN
 ENSG00000116649,SRM,TN,TN,TN,TN,TN
-ENSG00000116704,SLC35D1,TN,TN,FP,FP,TN
+ENSG00000116704,SLC35D1,TN,FP,TN,FP,TN
 ENSG00000116711,PLA2G4A,TN,TN,TN,TN,TN
 ENSG00000116745,RPE65,TN,TN,TN,TN,TN
 ENSG00000116748,AMPD1,TN,TN,TN,TN,TN
 ENSG00000116761,CTH,TN,TN,TN,TN,TN
 ENSG00000116771,AGMAT,TN,TN,TN,TN,TN
 ENSG00000116791,CRYZ,TN,TN,TN,TN,TN
-ENSG00000116906,GNPAT,TN,TN,FP,TN,TN
+ENSG00000116906,GNPAT,FP,TN,TN,TN,FP
 ENSG00000116981,NT5C1A,TN,TN,TN,TN,TN
 ENSG00000116984,MTR,TN,TN,TN,TN,TN
 ENSG00000117009,KMO,TN,TN,TN,TN,TN
@@ -899,14 +899,14 @@ ENSG00000117308,GALE,TN,TN,TN,TN,TN
 ENSG00000117394,SLC2A1,TN,TN,TN,TN,TN
 ENSG00000117410,ATP6V0B,FN,FN,FN,FN,FN
 ENSG00000117411,B4GALT2,TN,TN,TN,TN,FN
-ENSG00000117448,AKR1A1,TN,TN,FP,TN,TN
+ENSG00000117448,AKR1A1,FP,TN,TN,FP,FP
 ENSG00000117450,PRDX1,TN,TN,FN,TN,TN
 ENSG00000117461,PIK3R3,TN,TN,TN,TN,TN
 ENSG00000117479,SLC19A2,TN,FP,FP,FP,FP
 ENSG00000117480,FAAH,TN,TN,TN,TN,TN
 ENSG00000117528,ABCD3,TN,TN,TN,TN,TN
 ENSG00000117543,DPH5,FN,TN,FN,FN,TN
-ENSG00000117592,PRDX6,TN,FP,FP,FP,TN
+ENSG00000117592,PRDX6,TN,TN,FP,FP,FP
 ENSG00000117594,HSD11B1,TN,TN,TN,TN,TN
 ENSG00000117600,PLPPR4,.,.,.,.,.
 ENSG00000117643,MAN1C1,TN,TN,TN,TN,TN
@@ -954,7 +954,7 @@ ENSG00000120137,PANK3,TN,TN,TN,TN,TN
 ENSG00000120253,NUP43,TP,FP,TP,TP,TP
 ENSG00000120254,MTHFD1L,TN,TN,TN,TN,FN
 ENSG00000120265,PCMT1,TN,TN,TN,TN,TN
-ENSG00000120329,SLC25A2,TN,TN,FP,FP,TN
+ENSG00000120329,SLC25A2,TN,FP,TN,TN,FP
 ENSG00000120437,ACAT2,FP,FP,FP,FP,FP
 ENSG00000120563,LYZL1,.,.,.,.,.
 ENSG00000120697,ALG5,TN,TN,TN,TN,TN
@@ -986,7 +986,7 @@ ENSG00000122642,FKBP9,TN,TN,TN,TN,TN
 ENSG00000122643,NT5C3A,.,.,TN,TN,.
 ENSG00000122678,POLM,TN,TN,TN,TN,TN
 ENSG00000122729,ACO1,TN,TN,TN,TN,TN
-ENSG00000122787,AKR1D1,TN,TN,TN,TN,TN
+ENSG00000122787,AKR1D1,TN,TN,TN,FP,TN
 ENSG00000122824,NUDT10,.,.,.,.,.
 ENSG00000122863,CHST3,TN,TN,TN,TN,TN
 ENSG00000122884,P4HA1,TN,TN,TN,TN,TN
@@ -1000,7 +1000,7 @@ ENSG00000123453,SARDH,TN,TN,TN,TN,TN
 ENSG00000123454,DBH,TN,TN,TN,TN,TN
 ENSG00000123505,AMD1,TN,FP,FN,TN,FP
 ENSG00000123552,USP45,TN,TN,TN,TN,TN
-ENSG00000123643,SLC36A1,TN,FP,FP,FP,TN
+ENSG00000123643,SLC36A1,TN,FP,FP,FP,FP
 ENSG00000123684,LPGAT1,TN,TN,TN,TN,TN
 ENSG00000123739,PLA2G12A,.,.,TN,TN,.
 ENSG00000123836,PFKFB2,TN,TN,TN,TN,TN
@@ -1035,8 +1035,8 @@ ENSG00000124615,MOCS1,TN,TN,TN,TN,TN
 ENSG00000124713,GNMT,TN,TN,TN,TN,TN
 ENSG00000124767,GLO1,TN,TN,TN,TN,TN
 ENSG00000124789,NUP153,TP,TP,TP,TP,TP
-ENSG00000125166,GOT2,TN,TN,FP,FP,TN
-ENSG00000125246,CLYBL,TN,TN,FP,FP,TN
+ENSG00000125166,GOT2,TN,FP,TN,TN,FP
+ENSG00000125246,CLYBL,TN,TN,FP,TN,TN
 ENSG00000125255,SLC10A2,TN,TN,TN,TN,TN
 ENSG00000125257,ABCC4,TN,TN,TN,TN,TN
 ENSG00000125356,NDUFA1,TN,TN,FN,TN,TN
@@ -1087,7 +1087,7 @@ ENSG00000128708,HAT1,TN,TN,TN,TN,TN
 ENSG00000128731,HERC2,TN,TN,TN,TN,TN
 ENSG00000128918,ALDH1A2,FP,FP,TN,TN,TN
 ENSG00000128928,IVD,TN,TN,TN,TN,TN
-ENSG00000128951,DUT,TN,TN,TN,TN,TN
+ENSG00000128951,DUT,TN,TN,FP,FP,FP
 ENSG00000129128,SPCS3,TP,TP,TP,TP,TP
 ENSG00000129151,BBOX1,FP,FP,FP,FP,FP
 ENSG00000129167,TPH1,TN,TN,TN,TN,TN
@@ -1116,7 +1116,7 @@ ENSG00000130227,XPO7,TN,TN,TN,TN,TN
 ENSG00000130234,ACE2,TN,TN,TN,TN,TN
 ENSG00000130304,SLC27A1,TN,TN,TN,TN,TN
 ENSG00000130309,COLGALT1,TN,TN,TN,TN,TN
-ENSG00000130313,PGLS,TN,FN,FN,TP,TN
+ENSG00000130313,PGLS,TN,FN,FN,FN,TN
 ENSG00000130377,ACSBG2,TN,TN,TN,TN,TN
 ENSG00000130383,FUT5,TN,TN,TN,TN,TN
 ENSG00000130414,NDUFA10,TN,FN,FN,TN,TN
@@ -1172,7 +1172,7 @@ ENSG00000131873,CHSY1,TN,TN,TN,TN,TN
 ENSG00000131979,GCH1,FP,FP,FP,FP,FP
 ENSG00000132164,SLC6A11,TN,TN,TN,TN,TN
 ENSG00000132182,NUP210,FP,FP,FP,FP,FP
-ENSG00000132196,HSD17B7,P,P,P,P,P
+ENSG00000132196,HSD17B7,.,P,P,P,P
 ENSG00000132256,TRIM5,TN,TN,TN,TN,TN
 ENSG00000132330,SCLY,TN,TN,TN,TN,TN
 ENSG00000132376,INPP5K,TN,TN,TN,TN,TN
@@ -1254,7 +1254,7 @@ ENSG00000135241,PNPLA8,TN,FN,TN,TN,TN
 ENSG00000135318,NT5E,TN,TN,TN,TN,TN
 ENSG00000135390,ATP5MC2,FP,FP,TP,TP,FP
 ENSG00000135423,GLS2,FN,TN,TN,TN,TN
-ENSG00000135437,RDH5,TN,TP,FP,TP,FP
+ENSG00000135437,RDH5,FP,TP,FP,TP,FP
 ENSG00000135454,B4GALNT1,TN,TN,TN,TN,TN
 ENSG00000135587,SMPD2,TN,TN,TN,TN,TN
 ENSG00000135655,USP15,TN,TN,TN,TN,TN
@@ -1299,7 +1299,7 @@ ENSG00000136840,ST6GALNAC4,TN,TN,TN,TN,TN
 ENSG00000136856,SLC2A8,TN,TN,TN,TN,TN
 ENSG00000136868,SLC31A1,TN,TN,FN,TN,TN
 ENSG00000136872,ALDOB,TN,TN,TN,TN,TN
-ENSG00000136877,FPGS,FN,FP,FP,TP,TN
+ENSG00000136877,FPGS,FN,FP,FP,TP,FP
 ENSG00000136878,USP20,TN,TN,TN,TN,TN
 ENSG00000136881,BAAT,TN,TN,TN,TN,TN
 ENSG00000136888,ATP6V1G1,FN,TN,FN,TN,FN
@@ -1307,7 +1307,7 @@ ENSG00000136908,DPM2,TN,FN,TN,TN,TN
 ENSG00000136943,CTSV,TN,TN,TN,TN,TN
 ENSG00000136960,ENPP2,TN,TN,TN,TN,TN
 ENSG00000137054,POLR1E,TP,TP,TP,FP,TP
-ENSG00000137106,GRHPR,TN,TN,TN,TN,TN
+ENSG00000137106,GRHPR,TN,TN,TN,TN,FP
 ENSG00000137124,ALDH1B1,TN,TN,TN,TN,TN
 ENSG00000137168,PPIL1,TN,TN,TN,TN,TN
 ENSG00000137198,GMPR,TN,TN,TN,TN,TN
@@ -1317,7 +1317,7 @@ ENSG00000137364,TPMT,TN,TN,TN,TN,TN
 ENSG00000137392,CLPS,TN,TN,TN,TN,TN
 ENSG00000137393,RNF144B,TN,TN,TN,TN,TN
 ENSG00000137491,SLCO2B1,TN,TN,TN,TN,TN
-ENSG00000137563,GGH,TN,TP,FP,FP,TN
+ENSG00000137563,GGH,TN,TP,FP,FP,FP
 ENSG00000137714,FDX1,TN,TN,.,TN,TN
 ENSG00000137731,FXYD2,TN,TN,TN,TN,TN
 ENSG00000137767,SQOR,.,.,.,.,.
@@ -1325,13 +1325,13 @@ ENSG00000137770,CTDSPL2,.,.,TN,TN,.
 ENSG00000137817,PARP6,TN,TN,TN,TN,TN
 ENSG00000137825,ITPKA,TN,TN,TN,TN,TN
 ENSG00000137841,PLCB2,TN,TN,TN,FN,TN
-ENSG00000137857,DUOX1,TN,TN,TN,FP,TN
+ENSG00000137857,DUOX1,TN,TN,TN,TN,TN
 ENSG00000137860,SLC28A2,TN,TN,TN,TN,TN
 ENSG00000137868,STRA6,TN,TN,TN,TN,TN
 ENSG00000137869,CYP19A1,TN,TN,TN,TN,TN
 ENSG00000137944,KYAT3,TN,TN,TN,TN,TN
 ENSG00000137968,SLC44A5,TN,TN,TN,TN,TN
-ENSG00000137992,DBT,TN,TN,FP,FP,TN
+ENSG00000137992,DBT,TN,FP,TN,TN,FP
 ENSG00000137996,RTCA,TN,TN,TN,TN,TN
 ENSG00000138018,SELENOI,TN,TN,TN,TN,TN
 ENSG00000138029,HADHB,FP,FP,FP,FP,FP
@@ -1354,7 +1354,7 @@ ENSG00000138376,BARD1,TN,FN,FN,FN,FN
 ENSG00000138398,PPIG,TN,TN,TN,TN,TN
 ENSG00000138400,MDH1B,TN,TN,TN,TN,TN
 ENSG00000138411,HECW2,TN,TN,TN,TN,TN
-ENSG00000138413,IDH1,TN,TN,TN,TN,TN
+ENSG00000138413,IDH1,TN,TN,TN,FP,TN
 ENSG00000138449,SLC40A1,TN,TN,TN,TN,TN
 ENSG00000138496,PARP9,TN,TN,TN,TN,TN
 ENSG00000138592,USP8,FN,FN,TN,FN,FN
@@ -1414,7 +1414,7 @@ ENSG00000140284,SLC27A2,TN,TN,TN,TN,TN
 ENSG00000140287,HDC,TN,TN,TN,TN,TN
 ENSG00000140297,GCNT3,TN,TN,TN,TN,TN
 ENSG00000140367,UBE2Q2,TN,TN,TN,TN,TN
-ENSG00000140374,ETFA,TN,TN,TN,TN,TN
+ENSG00000140374,ETFA,FP,FP,FP,FP,FP
 ENSG00000140400,MAN2C1,TN,TN,TN,TN,TN
 ENSG00000140455,USP3,TN,TN,TN,TN,TN
 ENSG00000140459,CYP11A1,FN,TN,TN,TN,TN
@@ -1475,7 +1475,7 @@ ENSG00000143036,SLC44A3,TN,TN,TN,TN,TN
 ENSG00000143149,ALDH9A1,FP,FP,FP,FP,FP
 ENSG00000143153,ATP1B1,TN,TN,TN,TN,TN
 ENSG00000143156,NME7,TN,TN,TN,TN,TN
-ENSG00000143158,MPC2,TN,TN,TN,FP,TN
+ENSG00000143158,MPC2,TN,TN,TN,TN,TN
 ENSG00000143179,UCK2,TN,TN,TN,TN,TN
 ENSG00000143198,MGST3,TN,TN,TN,TN,TN
 ENSG00000143199,ADCY10,TN,TN,TN,TN,TN
@@ -1502,7 +1502,7 @@ ENSG00000143641,GALNT2,TN,TN,TN,TN,TN
 ENSG00000143653,SCCPDH,TN,TN,TN,TN,TN
 ENSG00000143753,DEGS1,TN,FP,TN,FP,FP
 ENSG00000143772,ITPKB,TN,TN,TN,TN,TN
-ENSG00000143774,GUK1,TP,FN,TP,TP,FN
+ENSG00000143774,GUK1,TP,FN,FN,TP,TP
 ENSG00000143797,MBOAT2,TN,FN,TN,TN,TN
 ENSG00000143799,PARP1,TN,TN,TN,TN,TN
 ENSG00000143811,PYCR2,TN,TN,TN,TN,TN
@@ -1613,7 +1613,7 @@ ENSG00000148834,GSTO1,TN,TN,FN,TN,TN
 ENSG00000149016,TUT1,FN,FN,FN,FN,FN
 ENSG00000149084,HSD17B12,FP,TP,FP,TP,FP
 ENSG00000149089,APIP,.,P,TN,TN,P
-ENSG00000149091,DGKZ,FP,TN,TN,TN,TN
+ENSG00000149091,DGKZ,TN,TN,TN,TN,TN
 ENSG00000149124,GLYAT,TN,TN,TN,TN,TN
 ENSG00000149150,SLC43A1,TN,TN,TN,TN,TN
 ENSG00000149313,AASDHPPT,FN,FN,FN,FN,FN
@@ -1640,7 +1640,7 @@ ENSG00000151012,SLC7A11,TN,TN,TN,TN,TN
 ENSG00000151092,NGLY1,TN,FN,FN,TN,TN
 ENSG00000151093,OXSM,FN,FN,TN,TN,FN
 ENSG00000151148,UBE3B,TN,TN,TN,TN,TN
-ENSG00000151151,IPMK,FP,TN,TN,TN,TN
+ENSG00000151151,IPMK,TN,TN,TN,TN,TN
 ENSG00000151224,MAT1A,TN,TN,TN,TN,TN
 ENSG00000151229,SLC2A13,TN,FN,TN,TN,TN
 ENSG00000151348,EXT2,TN,TN,TN,TN,TN
@@ -1726,7 +1726,7 @@ ENSG00000155897,ADCY8,TN,TN,TN,TN,TN
 ENSG00000156006,NAT2,TN,TN,TN,TN,TN
 ENSG00000156096,UGT2B4,TN,TN,TN,TN,TN
 ENSG00000156110,ADK,TN,TN,TN,TN,TN
-ENSG00000156136,DCK,FP,FP,TN,TN,FP
+ENSG00000156136,DCK,TN,TN,FP,FP,FP
 ENSG00000156219,ART3,TN,TN,TN,TN,TN
 ENSG00000156222,SLC28A1,TN,TN,TN,TN,TN
 ENSG00000156256,USP16,TN,TN,TN,TN,TN
@@ -1753,7 +1753,7 @@ ENSG00000157045,NTAN1,TN,TN,TN,TN,TN
 ENSG00000157064,NMNAT2,TN,TN,TN,TN,TN
 ENSG00000157087,ATP2B2,TN,TN,TN,TN,TN
 ENSG00000157103,SLC6A1,TN,TN,TN,TN,TN
-ENSG00000157184,CPT2,FP,TN,FP,FP,TN
+ENSG00000157184,CPT2,FP,FP,FP,FP,TN
 ENSG00000157326,DHRS4,TN,TN,TN,TN,TN
 ENSG00000157349,DDX19B,TP,FP,FP,FP,FP
 ENSG00000157350,ST3GAL2,TN,TN,TN,TN,TN
@@ -1798,7 +1798,7 @@ ENSG00000159339,PADI4,TN,TN,TN,TN,TN
 ENSG00000159348,CYB5R1,TN,TN,TN,TN,TN
 ENSG00000159398,CES5A,TN,TN,TN,TN,TN
 ENSG00000159399,HK2,FN,TN,TN,TN,TN
-ENSG00000159423,ALDH4A1,FP,TN,FP,FP,TN
+ENSG00000159423,ALDH4A1,FP,FP,FP,TN,FP
 ENSG00000159433,STARD9,TN,TN,TN,TN,TN
 ENSG00000159445,THEM4,TN,TN,TN,TN,TN
 ENSG00000159459,UBR1,TN,TN,TN,TN,TN
@@ -1820,7 +1820,7 @@ ENSG00000160191,PDE9A,TN,TN,TN,TN,TN
 ENSG00000160194,NDUFV3,TN,TN,TN,TN,TN
 ENSG00000160200,CBS,TN,TN,TN,TN,TN
 ENSG00000160209,PDXK,FP,FP,FP,FP,FP
-ENSG00000160211,G6PD,FN,FN,FN,TP,FN
+ENSG00000160211,G6PD,FN,FN,FN,FN,FN
 ENSG00000160216,AGPAT3,TN,TN,TN,TN,TN
 ENSG00000160282,FTCD,TN,TN,TN,TN,FN
 ENSG00000160285,LSS,FP,TP,FP,FP,FP
@@ -1844,7 +1844,7 @@ ENSG00000161267,BDH1,TN,TN,TN,TN,TN
 ENSG00000161281,COX7A1,TN,TN,TN,TN,TN
 ENSG00000161513,FDXR,TN,TN,FN,FN,TN
 ENSG00000161533,ACOX1,FP,TP,FP,FP,FP
-ENSG00000161653,NAGS,TN,TN,FP,FP,TN
+ENSG00000161653,NAGS,TN,FP,TN,TN,FP
 ENSG00000161714,PLCD3,TN,TN,TN,TN,TN
 ENSG00000161798,AQP5,TN,FN,TN,TN,TN
 ENSG00000161896,IP6K3,FN,TN,TN,TN,TN
@@ -1854,11 +1854,11 @@ ENSG00000162040,HS3ST6,TN,TN,TN,TN,TN
 ENSG00000162066,AMDHD2,TN,TN,TN,TN,FN
 ENSG00000162104,ADCY9,TN,TN,TN,TN,TN
 ENSG00000162139,NEU3,TN,TN,TN,TN,TN
-ENSG00000162174,ASRGL1,TN,TN,FP,TP,TN
+ENSG00000162174,ASRGL1,TN,FP,TN,FN,FP
 ENSG00000162298,SYVN1,FN,FN,TN,FN,TN
 ENSG00000162341,TPCN2,TN,TN,TN,TN,TN
 ENSG00000162365,CYP4A22,TN,TN,TN,TN,TN
-ENSG00000162368,CMPK1,P,P,FN,TP,P
+ENSG00000162368,CMPK1,P,.,TP,TP,P
 ENSG00000162383,SLC1A7,FN,TN,TN,TN,TN
 ENSG00000162390,ACOT11,TN,TN,TN,TN,TN
 ENSG00000162402,USP24,TN,TN,TN,TN,TN
@@ -2003,14 +2003,14 @@ ENSG00000165970,SLC6A5,TN,FN,TN,TN,TN
 ENSG00000165996,HACD1,TN,TN,TN,TN,TN
 ENSG00000166016,ABTB2,TN,TN,TN,TN,TN
 ENSG00000166035,LIPC,TN,TN,TN,TN,TN
-ENSG00000166123,GPT2,TN,TN,FP,FP,TN
+ENSG00000166123,GPT2,TN,FP,TN,TN,FP
 ENSG00000166126,AMN,TN,TN,TN,TN,TN
 ENSG00000166135,HIF1AN,TN,TN,TN,TN,TN
 ENSG00000166136,NDUFB8,FN,FN,FN,TN,FN
 ENSG00000166165,CKB,TN,TN,TN,TN,TN
 ENSG00000166169,POLL,TN,TN,TN,TN,TN
 ENSG00000166183,ASPG,TN,TN,TN,TN,TN
-ENSG00000166224,SGPL1,FP,TP,TN,FP,TN
+ENSG00000166224,SGPL1,TN,TP,FP,FP,TN
 ENSG00000166228,PCBD1,TN,TN,TN,TN,TN
 ENSG00000166262,FAM227B,TN,TN,TN,TN,TN
 ENSG00000166311,SMPD1,TN,TN,TN,TN,TN
@@ -2124,7 +2124,7 @@ ENSG00000169105,CHST14,TN,TN,TN,TN,TN
 ENSG00000169154,GOT1L1,TN,TN,TN,TN,TN
 ENSG00000169169,CPT1C,TN,TN,TN,TN,TN
 ENSG00000169180,XPO6,TN,TN,TN,TN,FN
-ENSG00000169239,CA5B,FP,FP,FP,FP,TN
+ENSG00000169239,CA5B,FP,FP,FP,TN,TN
 ENSG00000169255,B3GALNT1,TN,TN,TN,TN,TN
 ENSG00000169299,PGM2,TN,TN,TN,TN,TN
 ENSG00000169359,SLC33A1,TN,TN,TN,TN,TN
@@ -2189,7 +2189,7 @@ ENSG00000171408,PDE7B,TN,TN,TN,TN,TN
 ENSG00000171428,NAT1,.,.,.,.,.
 ENSG00000171453,POLR1C,TP,TP,TP,TP,TP
 ENSG00000171497,PPID,TN,TN,TN,TN,TN
-ENSG00000171503,ETFDH,TN,TN,TN,TN,TN
+ENSG00000171503,ETFDH,FP,FP,FP,FP,FP
 ENSG00000171560,FGA,TN,TN,TN,TN,TN
 ENSG00000171608,PIK3CD,TN,TN,TN,TN,TN
 ENSG00000171612,SLC25A33,TN,TN,TN,TN,TN
@@ -2257,7 +2257,7 @@ ENSG00000173486,FKBP2,TN,TN,TN,TN,TN
 ENSG00000173540,GMPPB,FN,FN,FN,FN,FN
 ENSG00000173597,SULT1B1,TN,TN,TN,TN,TN
 ENSG00000173598,NUDT4,TN,FN,FN,TN,TN
-ENSG00000173599,PC,FP,FP,TN,TP,TN
+ENSG00000173599,PC,FP,FP,FP,FN,TN
 ENSG00000173610,UGT2A1,TN,TN,TN,TN,TN
 ENSG00000173614,NMNAT1,TN,TN,TN,TN,TN
 ENSG00000173627,APOBEC4,TN,TN,TN,FN,TN
@@ -2333,7 +2333,7 @@ ENSG00000177054,ZDHHC13,TN,TN,TN,TN,TN
 ENSG00000177076,ACER2,TN,TN,TN,TN,TN
 ENSG00000177084,POLE,FN,TN,FN,TN,FN
 ENSG00000177108,ZDHHC22,TN,TN,TN,TN,TN
-ENSG00000177156,TALDO1,TN,TN,FP,FP,TN
+ENSG00000177156,TALDO1,TN,TN,FP,TN,TN
 ENSG00000177191,B3GNT8,TN,TN,TN,TN,TN
 ENSG00000177192,PUS1,FN,TN,TN,TN,TN
 ENSG00000177239,MAN1B1,TN,TN,TN,TN,TN
@@ -2341,7 +2341,7 @@ ENSG00000177414,UBE2U,.,.,TN,TN,.
 ENSG00000177465,ACOT4,TN,TN,TN,TN,TN
 ENSG00000177542,SLC25A22,FN,TN,TN,TN,FN
 ENSG00000177628,GBA,TN,TN,TN,TN,TN
-ENSG00000177646,ACAD9,TP,TN,TP,TN,TN
+ENSG00000177646,ACAD9,TP,FP,TP,TN,TN
 ENSG00000177666,PNPLA2,FN,TN,TN,TN,TN
 ENSG00000177669,MBOAT4,TN,TN,TN,TN,FN
 ENSG00000177700,POLR2L,TP,TP,TP,TP,TP
@@ -2350,7 +2350,7 @@ ENSG00000178035,IMPDH2,FN,TN,FN,TN,TN
 ENSG00000178127,NDUFV2,TN,TN,FN,TN,TN
 ENSG00000178234,GALNT11,TN,TN,TN,TN,TN
 ENSG00000178445,GLDC,TN,TN,TN,FP,TN
-ENSG00000178537,SLC25A20,FP,FP,FP,TN,FP
+ENSG00000178537,SLC25A20,FP,FP,FP,FP,FP
 ENSG00000178685,PARP10,TN,TN,TN,TN,TN
 ENSG00000178700,DHFR2,.,.,.,.,.
 ENSG00000178741,COX5A,FP,FP,TP,FP,TP
@@ -2408,11 +2408,11 @@ ENSG00000181873,IBA57,FN,FN,FN,FN,TN
 ENSG00000181915,ADO,TN,TN,TN,TN,FN
 ENSG00000182022,CHST15,TN,TN,TN,TN,TN
 ENSG00000182050,MGAT4C,TN,TN,TN,TN,TN
-ENSG00000182054,IDH2,TN,TN,FN,FN,TN
+ENSG00000182054,IDH2,TN,TN,FN,TP,TN
 ENSG00000182156,ENPP7,TN,FN,TN,TN,TN
 ENSG00000182179,UBA7,TN,TN,TN,TN,TN
 ENSG00000182197,EXT1,TN,TN,TN,TN,TN
-ENSG00000182199,SHMT2,TN,TN,FP,FP,TN
+ENSG00000182199,SHMT2,TN,FP,TN,TN,FP
 ENSG00000182224,CYB5D1,TN,TN,TN,TN,TN
 ENSG00000182247,UBE2E2,TN,TN,TN,TN,TN
 ENSG00000182272,B4GALNT4,FN,TN,TN,TN,TN
@@ -2588,7 +2588,7 @@ ENSG00000197253,TPSB2,.,.,.,.,.
 ENSG00000197296,FITM2,FN,FN,TN,TN,TN
 ENSG00000197323,TRIM33,TN,TN,TN,TN,TN
 ENSG00000197355,UAP1L1,TN,TN,TN,TN,TN
-ENSG00000197375,SLC22A5,TP,TP,TP,FP,FP
+ENSG00000197375,SLC22A5,TP,FN,TP,FP,FP
 ENSG00000197406,DIO3,TN,TN,TN,TN,TN
 ENSG00000197408,CYP2B6,TN,TN,TN,TN,TN
 ENSG00000197416,FABP12,TN,TN,FN,TN,TN
@@ -2624,7 +2624,7 @@ ENSG00000198077,CYP2A7,TN,TN,TN,TN,FN
 ENSG00000198088,NUP62CL,TN,TN,TN,TN,TN
 ENSG00000198099,ADH4,TN,TN,TN,TN,TN
 ENSG00000198108,CHSY3,TN,TN,TN,TN,TN
-ENSG00000198130,HIBCH,TN,TN,TN,FP,TN
+ENSG00000198130,HIBCH,TN,TN,TN,TN,TN
 ENSG00000198162,MAN1A2,TN,TN,TN,TN,TN
 ENSG00000198189,HSD17B11,TN,TN,TN,TN,TN
 ENSG00000198203,SULT1C2,TN,TN,TN,TN,TN
@@ -2735,7 +2735,7 @@ ENSG00000223443,USP17L2,.,.,.,.,.
 ENSG00000223572,CKMT1A,.,.,.,.,.
 ENSG00000223802,CERS1,TN,TN,TN,TN,TN
 ENSG00000224586,GPX5,TN,TN,TN,TN,TN
-ENSG00000225697,SLC26A6,TN,TN,TN,TN,TN
+ENSG00000225697,SLC26A6,TN,TN,TN,TN,FP
 ENSG00000226784,PGAM4,.,.,.,.,.
 ENSG00000227140,USP17L5,.,.,.,.,.
 ENSG00000227471,AKR1B15,.,.,.,.,.
@@ -2779,7 +2779,7 @@ ENSG00000241635,UGT1A1,.,.,.,.,.
 ENSG00000241644,INMT,TN,TN,TN,TN,TN
 ENSG00000241837,ATP5PO,P,P,TP,TP,P
 ENSG00000241878,PISD,TN,TN,FN,FN,FN
-ENSG00000241935,HOGA1,FP,TN,TN,FP,TN
+ENSG00000241935,HOGA1,FP,FP,FP,TN,FP
 ENSG00000241973,PI4KA,TN,FN,FN,FN,FN
 ENSG00000242110,AMACR,TN,TN,TN,TN,TN
 ENSG00000242366,UGT1A8,.,.,.,.,.
@@ -2790,7 +2790,7 @@ ENSG00000243480,AMY2A,.,.,.,.,.
 ENSG00000243678,NME2,TN,TN,TN,TN,TN
 ENSG00000243708,PLA2G4B,TN,TN,TN,TN,TN
 ENSG00000243955,GSTA1,.,.,.,.,.
-ENSG00000243989,ACY1,TN,TN,FP,FP,TN
+ENSG00000243989,ACY1,TN,FP,TN,TN,TN
 ENSG00000244005,NFS1,FN,FN,FN,FN,FN
 ENSG00000244038,DDOST,FN,FN,FN,FN,FN
 ENSG00000244067,GSTA2,.,.,.,.,.
@@ -2799,7 +2799,7 @@ ENSG00000244474,UGT1A4,.,.,.,.,.
 ENSG00000244486,SCARF2,TN,TN,TN,TN,TN
 ENSG00000247626,MARS2,FN,FN,FN,FN,TN
 ENSG00000247746,USP51,TN,TN,TN,TN,TN
-ENSG00000248098,BCKDHA,TN,TN,FP,FP,TN
+ENSG00000248098,BCKDHA,TN,FP,TN,TN,FP
 ENSG00000248144,ADH1C,TN,TN,TN,TN,TN
 ENSG00000248933,USP17L22,.,.,.,.,.
 ENSG00000249222,ATP5MGL,P,P,TP,FP,P
@@ -2844,6 +2844,6 @@ ENSG00000277161,PIGW,TN,TN,TN,TN,TN
 ENSG00000277494,GPIHBP1,TN,TN,TN,TN,TN
 ENSG00000277893,SRD5A2,.,.,.,.,.
 ENSG00000278540,ACACA,TP,TP,FP,FP,TP
-ENSG00000281500,SLC37A4,P,P,P,P,.
+ENSG00000281500,SLC37A4,P,P,P,P,P
 ENSG00000288702,UGT1A3,.,.,.,.,.
 ENSG00000288705,UGT1A5,.,.,.,.,.
diff --git a/data/testResults/gene-essential_summary.md b/data/testResults/gene-essential_summary.md
index 5a4f74d3..a989b0da 100644
--- a/data/testResults/gene-essential_summary.md
+++ b/data/testResults/gene-essential_summary.md
@@ -2,9 +2,9 @@
 
 | cellLine | TP | TN | FP | FN | accuracy | sensitivity | specificity | F1 | MCC |
 | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
-| DLD1 | 125 | 2172 | 124 | 224 | 0.8684 | 0.3582 | 0.946 | 0.4181 | 0.3525 |
-| GBM | 111 | 2145 | 138 | 251 | 0.8529 | 0.3066 | 0.9396 | 0.3633 | 0.2897 |
-| HCT116 | 141 | 2189 | 130 | 246 | 0.861 | 0.3643 | 0.9439 | 0.4286 | 0.3595 |
-| HELA | 114 | 2233 | 164 | 197 | 0.8667 | 0.3666 | 0.9316 | 0.3871 | 0.3132 |
-| RPE1 | 86 | 2183 | 162 | 214 | 0.8578 | 0.2867 | 0.9309 | 0.3139 | 0.2367 |
-| all | 59 | 2355 | 159 | 69 | 0.9137 | 0.4609 | 0.9368 | 0.341 | 0.3103 |
+| DLD1 | 124 | 2170 | 126 | 225 | 0.8673 | 0.3553 | 0.9451 | 0.414 | 0.3475 |
+| GBM | 110 | 2123 | 160 | 252 | 0.8442 | 0.3039 | 0.9299 | 0.3481 | 0.2654 |
+| HCT116 | 141 | 2195 | 124 | 246 | 0.8633 | 0.3643 | 0.9465 | 0.4325 | 0.3662 |
+| HELA | 108 | 2243 | 154 | 203 | 0.8682 | 0.3473 | 0.9358 | 0.377 | 0.3052 |
+| RPE1 | 87 | 2154 | 191 | 213 | 0.8473 | 0.29 | 0.9186 | 0.301 | 0.2156 |
+| all | 59 | 2351 | 163 | 69 | 0.9122 | 0.4609 | 0.9352 | 0.3371 | 0.3066 |