Baseline STARsolo mapping metrics (ce11/WS298) — 13 worm datasets, pre-3′UTR-extension

[lhqing]

Baseline for the 3′-UTR-extension benchmark — #52.

STARsolo mapping metrics for the 13 C. elegans single-cell datasets (14 pipelines, 138 samples), mapped against the stock ce11 / WS298 annotation — the before snapshot. Once we build an extended 3′-UTR GTF and re-quantify, we compare against these numbers to answer #52: does the gene count go up?

What to watch

A 3′-UTR extension changes feature assignment, not alignment, so the informative columns are:

• total_genes — genes detected per sample → expect ↑ if extended UTRs recover 3′ reads
• med_gene — median genes per cell → expect ↑
• feat_uniq — fraction of reads uniquely assigned to a gene feature → the direct lever (reads landing just past the current 3′ end get captured)
• genome_UM — genome mapping → expected flat (same alignment; only the GTF's feature intervals change). This is the control: any gene-count gain must come from annotation, not re-mapping.

Because alignment is unchanged, the re-quantification can likely run from the saved CRAMs without re-aligning (pending CB/UB tag retention — see #52).

Run config

genome ce11, annotation WS298, STARsolo; soloFeatures = Gene, GeneFull, GeneFull_ExonOverIntron, GeneFull_Ex50pAS, Velocyto. Primary feature = Gene (scRNA) / GeneFull (snRNA). All 14 pipelines finished EXIT=0; every sample produced .h5ad + .velocyto.h5ad + .cram + .qc.json.gz. Metrics are read from each sample's qc.json.gz; column legend + flag thresholds are at the bottom.

Baseline health: 0 SEVERE issues across 138 samples — 2 WARN (thin/low-input libraries) + 5 NOTE (shallow or undersequenced), all data-quality, none a pipeline fault. Machine-readable mapping_metrics.tsv accompanies this table.

---

Flagged samples (ranked)

sev	dataset	sample	issue
WARN	GSE136049 10x-3p-gex-v3	SAMN17106785	genome mapping 0.50 (uniq 0.46), valid_bc 0.865 vs ~0.97 in sibling v3 samples (28.8M reads with no whitelist match); cell-calling collapses to 239 cells at median 21692 UMI / 2877 genes. Raw features_stats (read on-node) show unmapped reads dominating — a genuinely weak/low-complexity library (low input, likely degraded/contaminated), NOT a pipeline or chemistry fault: barcodes resolved cleanly and all five soloFeatures computed. Retain with a data-quality caveat.
WARN	GSE229022	SAMN39550232	only 221 cells called — low-input/thin library
NOTE	GSE226715	SAMN33601518	saturation 0.12 — undersequenced (mapping itself fine)
NOTE	GSE226715	SAMN33601519	saturation 0.10 — undersequenced (mapping itself fine)
NOTE	GSE226715	SAMN33601520	saturation 0.09 — undersequenced (mapping itself fine)
NOTE	GSE310667	SAMN53327904	median 283 genes/cell — shallow/low-complexity
NOTE	GSE310667	SAMN53327905	median 138 genes/cell — shallow/low-complexity

GSE126954 — CLEAN

10x v2 (sci-RNA-seq origin) · Gene — 7/7 samples

sci-RNA-seq origin mapped as 10x-v2: valid barcodes 0.94–0.98 across all 7 samples confirm the barcodes hit the v2 whitelist cleanly, so the chemistry resolution holds. SAMN10988847 called only 507 cells at ~228k reads/cell — a cell-calling knee that landed high (deep, few cells), worth an eye downstream but barcodes/mapping are fine. (8 GEO GSMs → 7 samples: the over-length experiment was absorbed into v2, expected.)

sample	reads(M)	valid_bc	genome_UM	genome_uq	feat_uniq	sat	cells	med_UMI	med_gene	totGenes	frac_cells	flag
SAMN10988833	299	0.966	0.877	0.854	0.784	0.605	2808	7115	2204	18179	0.310	OK
SAMN10988843	152	0.952	0.901	0.874	0.797	0.790	8916	776	497	17894	0.391	OK
SAMN10988844	140	0.945	0.895	0.861	0.779	0.590	5786	2219	1100	18719	0.397	OK
SAMN10988845	188	0.983	0.926	0.857	0.792	0.668	6255	2841	1356	18498	0.464	OK
SAMN10988846	260	0.968	0.854	0.829	0.779	0.509	2300	10085	2703	18915	0.352	OK
SAMN10988847	374	0.973	0.877	0.855	0.797	0.794	507	25497	4250	18978	0.388	OK
SAMN10988848	347	0.972	0.914	0.878	0.810	0.640	2615	6462	2059	18470	0.234	OK

GSE136049 — MINOR NOTES

10x v2 + v3 (2 assays) · Gene · FACS-sorted neurons — 17/17 samples

CeNGEN FACS-sorted single-neuron-class libraries: the high saturation (~0.9–0.99) and large unique-vs-multi mapping gaps are the expected low-diversity, deeply-sequenced profile, not faults. INDEPENDENTLY VERIFIED (raw barcodes/features stats read on the node before it dropped).

assay	sample	reads(M)	valid_bc	genome_UM	genome_uq	feat_uniq	sat	cells	med_UMI	med_gene	totGenes	frac_cells	flag
10x-3p-gex-v2	SAMN12607287	336	0.978	0.931	0.878	0.785	0.939	2912	2850	858	17522	0.709	OK
10x-3p-gex-v2	SAMN12607288	712	0.980	0.906	0.582	0.525	0.983	2614	1190	379	16182	0.734	OK
10x-3p-gex-v2	SAMN12607289	684	0.980	0.911	0.573	0.518	0.982	2944	1105	353	15669	0.725	OK
10x-3p-gex-v2	SAMN12607290	234	0.978	0.869	0.816	0.705	0.964	3356	1237	326	14838	0.837	OK
10x-3p-gex-v2	SAMN12607291	624	0.984	0.904	0.805	0.732	0.964	3460	2433	609	17610	0.761	OK
10x-3p-gex-v2	SAMN12607292	366	0.983	0.899	0.772	0.704	0.979	2624	1085	447	14637	0.722	OK
10x-3p-gex-v2	SAMN12607293	577	0.983	0.878	0.735	0.653	0.917	7411	2463	666	18485	0.710	OK
10x-3p-gex-v2	SAMN12607294	325	0.983	0.898	0.567	0.505	0.976	2281	1052	329	13413	0.789	OK
10x-3p-gex-v2	SAMN12607295	262	0.981	0.882	0.849	0.759	0.989	1107	702	309	11900	0.663	OK
10x-3p-gex-v2	SAMN12607296	170	0.975	0.903	0.674	0.607	0.890	3802	1297	399	16654	0.677	OK
10x-3p-gex-v2	SAMN12607297	175	0.975	0.910	0.688	0.629	0.922	2696	1382	421	16348	0.640	OK
10x-3p-gex-v3	SAMN12607285	434	0.969	0.932	0.774	0.682	0.974	2068	1807	636	15623	0.724	OK
10x-3p-gex-v3	SAMN12607286	743	0.979	0.963	0.802	0.692	0.941	1374	4316	1386	17979	0.327	OK
10x-3p-gex-v3	SAMN17106782	297	0.969	0.963	0.863	0.786	0.903	2413	3627	924	17848	0.556	OK
10x-3p-gex-v3	SAMN17106783	395	0.979	0.953	0.900	0.815	0.920	2407	4599	1038	16919	0.585	OK
10x-3p-gex-v3	SAMN17106784	289	0.908	0.753	0.523	0.459	0.911	1607	2533	764	16262	0.577	OK
10x-3p-gex-v3	SAMN17106785	216	0.865	0.497	0.457	0.409	0.830	239	21692	2877	15963	0.534	WARN

GSE208154 — CLEAN

10x v3 (from possorted BAM) · Gene — 11/11 samples

Reconstructed from 10x possorted BAM (bamtofastq), multi-flowcell/multi-lane; was blocked as issue #30 and unblocked by fix F1. All 11 samples present with valid barcodes 0.96–0.98 — F1 seated the barcode read correctly and the index (I1) reads were dropped as intended.

sample	reads(M)	valid_bc	genome_UM	genome_uq	feat_uniq	sat	cells	med_UMI	med_gene	totGenes	frac_cells	flag
SAMN29720279	215	0.960	0.757	0.618	0.531	0.928	517	1920	890	16319	0.406	OK
SAMN29720280	224	0.976	0.909	0.828	0.749	0.873	832	4600	1580	19020	0.371	OK
SAMN29720281	290	0.981	0.933	0.875	0.792	0.754	995	12438	2805	20164	0.353	OK
SAMN29720282	233	0.981	0.942	0.885	0.810	0.763	1120	10679	2523	19885	0.438	OK
SAMN29720283	195	0.982	0.935	0.886	0.800	0.716	1353	7471	1856	20559	0.352	OK
SAMN29720284	223	0.982	0.943	0.884	0.784	0.724	3104	3870	1193	20274	0.358	OK
SAMN29720285	232	0.977	0.909	0.828	0.752	0.867	644	6421	1877	18495	0.382	OK
SAMN29720286	205	0.981	0.941	0.887	0.808	0.703	1148	10273	2451	19935	0.373	OK
SAMN29720287	179	0.980	0.943	0.888	0.813	0.727	1260	9250	2259	19953	0.449	OK
SAMN29720288	268	0.982	0.940	0.890	0.801	0.787	1522	7213	1838	20915	0.371	OK
SAMN29720289	246	0.982	0.951	0.891	0.799	0.762	3589	3503	1122	20117	0.387	OK

GSE208229 — CLEAN

10x v3 · GeneFull · snRNA — 31/31 samples

snRNA (GeneFull): low fraction-of-reads-in-cells (0.10–0.44) is the expected high-ambient single-nucleus signature, not a defect. Many samples are moderate-nuclei / very-deeply-sequenced (sorted nuclei). Sample count verified 31/31 (units.tsv + results + rows) before the node dropped.

sample	reads(M)	valid_bc	genome_UM	genome_uq	feat_uniq	sat	cells	med_UMI	med_gene	totGenes	frac_cells	flag
SAMN29755204	721	0.975	0.964	0.841	0.783	0.942	1124	3104	1527	18903	0.207	OK
SAMN29755206	714	0.958	0.938	0.611	0.556	0.979	1598	621	396	18804	0.259	OK
SAMN29755208	525	0.955	0.962	0.780	0.722	0.910	747	3552	1515	17076	0.221	OK
SAMN29755209	748	0.966	0.949	0.571	0.522	0.894	938	4571	1841	18818	0.196	OK
SAMN29755211	326	0.958	0.970	0.803	0.735	0.852	718	3642	1602	17889	0.178	OK
SAMN29755212	771	0.964	0.966	0.767	0.711	0.901	758	5505	2059	18325	0.170	OK
SAMN29755214	650	0.965	0.964	0.606	0.559	0.861	828	6786	2384	19139	0.210	OK
SAMN29755216	316	0.953	0.969	0.785	0.705	0.889	782	3183	1475	18414	0.243	OK
SAMN29755217	704	0.962	0.968	0.774	0.715	0.925	911	3789	1606	18491	0.217	OK
SAMN29755219	680	0.962	0.962	0.580	0.525	0.880	727	6473	2256	19444	0.227	OK
SAMN29755220	358	0.960	0.968	0.807	0.745	0.875	889	3774	1620	18125	0.244	OK
SAMN29755221	686	0.975	0.964	0.823	0.780	0.917	993	2902	1454	17661	0.119	OK
SAMN29755222	763	0.960	0.936	0.628	0.574	0.979	1209	739	478	17855	0.209	OK
SAMN29755223	608	0.952	0.902	0.672	0.617	0.918	1038	2611	1317	17941	0.176	OK
SAMN29755224	503	0.954	0.903	0.679	0.622	0.883	1251	2793	1451	18326	0.171	OK
SAMN29755225	657	0.976	0.949	0.823	0.780	0.896	1044	3497	1707	18118	0.126	OK
SAMN29755227	734	0.959	0.936	0.600	0.546	0.979	1118	739	475	18344	0.214	OK
SAMN29755229	576	0.952	0.903	0.662	0.605	0.905	1069	2651	1359	18144	0.175	OK
SAMN29755230	761	0.934	0.858	0.720	0.647	0.966	1474	3075	1332	20392	0.436	OK
SAMN29755232	831	0.949	0.907	0.783	0.732	0.957	354	6949	2407	17328	0.203	OK
SAMN29755233	423	0.969	0.962	0.905	0.865	0.895	556	3418	1539	16990	0.103	OK
SAMN29755235	570	0.975	0.952	0.890	0.849	0.898	513	6919	2591	19553	0.159	OK
SAMN29755236	493	0.974	0.959	0.870	0.828	0.906	510	5506	2214	19308	0.155	OK
SAMN29755238	582	0.975	0.947	0.854	0.814	0.940	437	5330	2036	18449	0.184	OK
SAMN29755239	432	0.969	0.965	0.906	0.865	0.880	643	5125	2076	18042	0.155	OK
SAMN29755241	717	0.975	0.952	0.878	0.839	0.922	621	6618	2407	19233	0.164	OK
SAMN29755242	679	0.978	0.954	0.879	0.837	0.864	915	12624	3538	21157	0.250	OK
SAMN29755244	744	0.980	0.952	0.684	0.643	0.894	573	9386	2994	21123	0.213	OK
SAMN29755247	1018	0.981	0.947	0.863	0.832	0.973	419	3491	1619	16253	0.139	OK
SAMN29755248	968	0.982	0.959	0.907	0.880	0.973	527	4463	1964	16793	0.222	OK
SAMN29755250	828	0.981	0.955	0.882	0.850	0.964	685	4435	1969	17898	0.239	OK

GSE226715 — MINOR NOTES

10x v3 · Gene · scRNA (shallow) — 3/3 samples

Whole-body N2 scRNA, deliberately shallow (30–67M reads): saturation 0.09–0.12 just means undersequenced — genome mapping (0.72–0.79) and per-cell complexity are otherwise healthy. A depth note, not a mapping fault.

sample	reads(M)	valid_bc	genome_UM	genome_uq	feat_uniq	sat	cells	med_UMI	med_gene	totGenes	frac_cells	flag
SAMN33601518	59	0.985	0.788	0.698	0.662	0.119	3591	3076	1078	17659	0.414	NOTE
SAMN33601519	67	0.979	0.718	0.539	0.504	0.103	1736	3569	1107	17411	0.303	NOTE
SAMN33601520	30	0.972	0.791	0.655	0.612	0.088	1460	3380	1082	15973	0.426	NOTE

GSE229022 — MINOR NOTES

10x v3 · GeneFull · snRNA (40 runs→28 samples) — 28/28 samples

snRNA aging atlas; 40 SRA runs correctly merge into 28 samples (verified units.tsv + results + rows before the node dropped). One low-input library (SAMN39550232, 221 cells) — barcodes 0.93 and genome mapping 0.95 are fine, so it's a thin library, not a pipeline fault.

sample	reads(M)	valid_bc	genome_UM	genome_uq	feat_uniq	sat	cells	med_UMI	med_gene	totGenes	frac_cells	flag
SAMN34081614	446	0.972	0.940	0.759	0.568	0.875	4950	1839	1143	29834	0.389	OK
SAMN34081615	506	0.973	0.947	0.822	0.619	0.843	12426	1649	1031	29598	0.521	OK
SAMN34081616	501	0.973	0.967	0.794	0.617	0.880	6828	2058	1275	25646	0.477	OK
SAMN34081617	486	0.970	0.959	0.798	0.597	0.924	4181	1297	860	25161	0.357	OK
SAMN34081618	503	0.970	0.965	0.793	0.611	0.881	10843	1454	1000	25739	0.518	OK
SAMN34081619	489	0.965	0.949	0.775	0.579	0.839	11934	1517	997	29403	0.527	OK
SAMN34081620	645	0.972	0.975	0.810	0.599	0.887	3374	3467	1927	26415	0.382	OK
SAMN34081621	288	0.976	0.958	0.839	0.635	0.811	8327	1311	897	27308	0.412	OK
SAMN34081622	485	0.966	0.909	0.597	0.460	0.926	2388	1340	774	28042	0.320	OK
SAMN34081623	518	0.973	0.916	0.651	0.529	0.898	2670	2279	1195	29185	0.330	OK
SAMN34081624	569	0.973	0.950	0.827	0.614	0.922	4542	1790	1149	27096	0.421	OK
SAMN34081625	492	0.967	0.958	0.856	0.694	0.790	5712	1878	1265	27078	0.203	OK
SAMN34081626	671	0.966	0.934	0.796	0.599	0.918	5154	1714	1068	28362	0.355	OK
SAMN34081627	477	0.966	0.952	0.758	0.573	0.885	5886	1748	1089	27925	0.461	OK
SAMN34081628	624	0.974	0.960	0.826	0.623	0.887	5860	2869	1664	29427	0.504	OK
SAMN34081629	519	0.973	0.944	0.779	0.602	0.860	6472	1856	1167	30344	0.362	OK
SAMN34081630	511	0.966	0.963	0.842	0.677	0.828	11519	1179	745	27993	0.304	OK
SAMN34081631	524	0.967	0.940	0.774	0.596	0.870	7442	1851	1141	28161	0.462	OK
SAMN34081632	469	0.973	0.951	0.816	0.610	0.860	6480	2502	1516	28811	0.527	OK
SAMN39550230	249	0.943	0.929	0.574	0.390	0.794	6970	753	514	26769	0.354	OK
SAMN39550231	251	0.925	0.939	0.722	0.499	0.858	1251	1964	1132	22778	0.214	OK
SAMN39550232	238	0.926	0.950	0.691	0.505	0.868	221	5561	2303	22417	0.317	WARN
SAMN39550233	347	0.935	0.951	0.612	0.428	0.901	458	2865	1482	21884	0.255	OK
SAMN39550234	357	0.941	0.958	0.808	0.588	0.894	5132	1070	774	26138	0.344	OK
SAMN39550235	342	0.939	0.962	0.807	0.572	0.889	5210	1044	764	26007	0.344	OK
SAMN39550236	409	0.942	0.962	0.776	0.580	0.911	4893	776	557	26287	0.252	OK
SAMN39550237	334	0.921	0.957	0.761	0.571	0.819	1417	3037	1808	20983	0.200	OK
SAMN39550238	354	0.930	0.941	0.755	0.579	0.795	1566	3579	2044	21899	0.210	OK

GSE234962 — CLEAN

10x v3 · Gene · scRNA — 4/4 samples

Motor-neuron scRNA, all 4 samples healthy; a couple are oversequenced (saturation ~0.97) with deep cells — expected.

sample	reads(M)	valid_bc	genome_UM	genome_uq	feat_uniq	sat	cells	med_UMI	med_gene	totGenes	frac_cells	flag
SAMN35739865	416	0.975	0.937	0.855	0.750	0.952	2572	2572	885	16127	0.615	OK
SAMN35739866	201	0.977	0.931	0.832	0.725	0.868	3283	2534	849	16235	0.585	OK
SAMN35739867	447	0.978	0.948	0.845	0.753	0.970	815	2965	901	13871	0.413	OK
SAMN35739868	507	0.980	0.947	0.843	0.751	0.976	1083	2347	784	13936	0.437	OK

GSE256266 — CLEAN

10x v3 · GeneFull · snRNA (glia) — 4/4 samples

Glia snRNA (GeneFull): 2 of 4 samples (SAMN40022216/217) run a bit lower on genome mapping (0.73–0.78) and Q30 — read-quality-driven, still within usable range; barcodes 0.95.

sample	reads(M)	valid_bc	genome_UM	genome_uq	feat_uniq	sat	cells	med_UMI	med_gene	totGenes	frac_cells	flag
SAMN40022214	72	0.944	0.929	0.668	0.617	0.389	5136	1473	580	19982	0.378	OK
SAMN40022215	91	0.956	0.931	0.683	0.638	0.426	4837	1806	676	20494	0.360	OK
SAMN40022216	98	0.949	0.775	0.594	0.555	0.407	7833	1165	460	19169	0.361	OK
SAMN40022217	87	0.948	0.728	0.556	0.519	0.344	9337	946	394	18973	0.373	OK

GSE274290 — CLEAN

BD Rhapsody WTA · Gene — 1/1 samples

The sole BD Rhapsody WTA dataset: valid barcodes 0.897 (normal for BD's CLS whitelist), 14.9k cells, median 2933 genes/cell — the BD Rhapsody chemistry mapped correctly.

sample	reads(M)	valid_bc	genome_UM	genome_uq	feat_uniq	sat	cells	med_UMI	med_gene	totGenes	frac_cells	flag
SAMN43079677	840	0.897	0.847	0.810	0.650	0.564	14852	11704	2933	17030	0.830	OK

GSE310667 — MINOR NOTES

10x v3 · Gene · scRNA — 16/16 samples

Juvenile-neuron scRNA, all 16 present; a couple of shallow/low-complexity libraries (SAMN53327904/905, median 138–283 genes/cell) — thin cells, not mapping faults. Multimapping gaps are the low-complexity neuron profile.

sample	reads(M)	valid_bc	genome_UM	genome_uq	feat_uniq	sat	cells	med_UMI	med_gene	totGenes	frac_cells	flag
SAMN53327892	950	0.977	0.850	0.585	0.493	0.972	4408	1176	398	16611	0.525	OK
SAMN53327893	197	0.965	0.864	0.588	0.506	0.954	1086	951	359	14575	0.448	OK
SAMN53327894	695	0.972	0.926	0.730	0.607	0.886	6043	4268	1323	18013	0.705	OK
SAMN53327895	631	0.979	0.957	0.761	0.677	0.857	9906	4426	1456	16552	0.832	OK
SAMN53327896	477	0.969	0.906	0.642	0.529	0.892	3520	2834	1051	16252	0.513	OK
SAMN53327897	510	0.968	0.831	0.612	0.534	0.950	5669	1558	698	15721	0.832	OK
SAMN53327898	558	0.968	0.911	0.758	0.654	0.861	4741	5951	1005	18257	0.593	OK
SAMN53327899	522	0.951	0.893	0.611	0.539	0.944	2430	1738	615	15046	0.375	OK
SAMN53327900	435	0.975	0.907	0.714	0.619	0.951	2611	1783	647	16946	0.539	OK
SAMN53327901	217	0.968	0.927	0.724	0.626	0.741	6024	3188	862	16761	0.711	OK
SAMN53327902	610	0.972	0.948	0.817	0.727	0.923	7143	2088	679	17358	0.695	OK
SAMN53327903	340	0.964	0.921	0.709	0.614	0.908	1916	2618	941	17105	0.428	OK
SAMN53327904	83	0.987	0.919	0.870	0.720	0.913	5301	666	283	14522	0.853	NOTE
SAMN53327905	76	0.976	0.897	0.824	0.658	0.959	5162	251	138	12646	0.825	NOTE
SAMN53327906	401	0.977	0.827	0.685	0.592	0.938	4995	1545	658	18305	0.717	OK
SAMN53327907	422	0.980	0.926	0.737	0.636	0.929	4354	1460	615	17285	0.476	OK

PRJNA1027859 — CLEAN

10x v3 · GeneFull · snRNA (demo) — 6/6 samples

snRNA neuron atlas (seqforge demo), all 6 healthy; GeneFull-primary as intended.

sample	reads(M)	valid_bc	genome_UM	genome_uq	feat_uniq	sat	cells	med_UMI	med_gene	totGenes	frac_cells	flag
SAMN40935616	455	0.979	0.897	0.778	0.651	0.852	17722	1083	670	29139	0.548	OK
SAMN40935617	536	0.953	0.902	0.579	0.479	0.935	7367	724	429	26142	0.451	OK
SAMN40935618	505	0.970	0.931	0.832	0.713	0.901	4860	1698	955	26092	0.313	OK
SAMN40935619	512	0.979	0.909	0.819	0.679	0.888	11178	1308	797	29180	0.481	OK
SAMN40935620	520	0.961	0.876	0.674	0.556	0.916	5013	1267	754	26887	0.377	OK
SAMN40935621	524	0.973	0.926	0.846	0.715	0.908	7549	1292	792	27309	0.375	OK

PRJNA1195922 — CLEAN

10x v3 · GeneFull · snRNA (male) — 8/8 samples

Male-neuron snRNA, all 8 present; larger unique-vs-multi gaps and lower feat_uniq are the low-complexity/repeat neuron profile, within snRNA range. (SAMN49549038 sex=male is a metadata fix, F4 — not a QC signal.)

sample	reads(M)	valid_bc	genome_UM	genome_uq	feat_uniq	sat	cells	med_UMI	med_gene	totGenes	frac_cells	flag
SAMN49549035	290	0.968	0.925	0.808	0.693	0.778	6763	1463	819	25285	0.280	OK
SAMN49549036	256	0.974	0.903	0.810	0.693	0.829	15290	803	501	26133	0.502	OK
SAMN49549037	498	0.974	0.948	0.842	0.711	0.945	13008	630	404	26602	0.548	OK
SAMN49549038	276	0.969	0.928	0.783	0.668	0.797	2653	2433	1369	25004	0.235	OK
SAMN49549039	200	0.970	0.884	0.783	0.625	0.853	7651	742	522	25084	0.404	OK
SAMN49549040	477	0.969	0.953	0.870	0.579	0.914	10579	794	572	28595	0.455	OK
SAMN49549041	431	0.970	0.934	0.854	0.627	0.921	11371	679	481	27636	0.456	OK
SAMN49569331	420	0.969	0.936	0.857	0.630	0.931	11838	615	443	27609	0.517	OK

PRJNA658829 — CLEAN

10x v3 · Gene · scRNA (eQTL; 6 runs→2 BioSamples) — 2/2 samples

CRITICAL CHECK — RESOLVED. Both samples show valid barcodes 0.96/0.97, so fix F1 seated the barcode read on _2 correctly; the earlier near-zero-barcode concern does NOT materialize. 6 runs group into 2 BioSamples (SAMN15970313 ~2.2B reads; SAMN15970314 lower median genes/cell — a thinner library, but barcodes are valid).

sample	reads(M)	valid_bc	genome_UM	genome_uq	feat_uniq	sat	cells	med_UMI	med_gene	totGenes	frac_cells	flag
SAMN15970313	2226	0.963	0.932	0.776	0.693	0.686	7039	15853	2145	19916	0.292	OK
SAMN15970314	595	0.972	0.882	0.617	0.566	0.342	14873	3382	437	19920	0.322	OK

Appendix — all 138 samples (concatenated)

Full machine-readable table: mapping_metrics.tsv (same directory). Columns: dataset, assay, sample, feat(ure), n_reads, valid_bc, genome_UM/uniq, feat_uniq, saturation, q30_cbumi/rna, est_cells, mean_reads_cell, median_umi/gene_cell, total_genes, frac_reads_cells.

Flag thresholds: SEVERE = valid_bc<0.40 or genome_UM<0.30; WARN = valid_bc<0.70, genome_UM<0.60, feat_uniq<0.20, or cells<300; NOTE = median_gene<300 (shallow) or saturation<0.12 (undersequenced). snRNA (GeneFull) datasets aren't flagged for low feat_uniq or high ambient, which are expected for single-nucleus.