Workflow: expression values from HPC RGD workflow (processed before workflow 2.1); computed sex, strand and library prep added by RGD attribute backfill 1.0 (2026-10-20) using the workflow 2.1 rules. Note: ComputedSex is called from sex-gene expression: R = (Xist TPM + 1) / (median TPM of Uty, Ddx3y, Kdm5d and Eif2s3y + 1); R >= 10 is called F, R <= 1 is called M, and other values, or samples where Xist and the Y-gene median are both below 1 TPM, are Undetermined. Females express Xist and males the Y-linked genes. Sry is reported but not used in the calculation. XYRatio (X:Y read coverage) is shown for reference only. Agreement compares ComputedSex with InputSex (submitted to GEO).
SampleID	InputSex	ComputedSex	XYRatio	Agreement	Xist	Uty	Sry	Ddx3y	Kdm5d	Eif2s3y	ComputedStrand	ComputedLibraryPrep	PctMRNA	PctIntronic	PctIntergenic	PctRibosomal	UniqPct	MultiPct	TooShortPct	NonPolyA_perM	LibraryPrepRule	LibraryPrepQC	LibraryPrepReason
GSM6994952	M	M	NA	Agree	0.00	4.13	0.00	15.56	5.94	19.99	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.58387	0.303857	0.067566	0.044706	92.53	5.78	0.69	1936	LP2 (2026-09-30)	PASS	NonPolyA_perM 1936 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994953	M	M	NA	Agree	0.00	4.55	0.00	17.23	6.37	23.40	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.560017	0.283199	0.068911	0.087873	88.31	10.02	0.66	1696	LP2 (2026-09-30)	PASS	NonPolyA_perM 1696 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994954	M	M	NA	Agree	0.00	5.85	0.00	20.71	8.26	25.88	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.521449	0.324058	0.068866	0.085627	88.46	9.76	0.73	1721	LP2 (2026-09-30)	PASS	NonPolyA_perM 1721 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994955	M	M	NA	Agree	0.01	4.98	0.00	16.28	6.82	19.87	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.538268	0.291562	0.071314	0.098857	87.23	11.14	0.63	1827	LP2 (2026-09-30)	PASS	NonPolyA_perM 1827 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994956	M	M	NA	Agree	0.00	5.93	0.00	23.05	8.52	32.08	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.578175	0.317319	0.068117	0.036389	93.44	5.03	0.68	1567	LP2 (2026-09-30)	PASS	NonPolyA_perM 1567 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994957	M	M	NA	Agree	0.02	6.31	0.00	24.01	8.51	31.38	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.641394	0.277067	0.06272	0.018819	94.51	3.65	0.69	5549	LP2 (2026-09-30)	PASS	NonPolyA_perM 5549 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994958	M	M	NA	Agree	0.00	5.53	0.00	18.41	7.81	25.17	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.563415	0.28288	0.063179	0.090526	88.03	10.37	0.68	5018	LP2 (2026-09-30)	PASS	NonPolyA_perM 5018 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994959	M	M	NA	Agree	0.01	3.12	0.00	13.58	5.39	16.84	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.564784	0.328309	0.056208	0.050699	91.57	6.62	0.80	3367	LP2 (2026-09-30)	PASS	NonPolyA_perM 3367 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994960	M	M	NA	Agree	0.02	4.82	0.00	15.05	6.34	20.89	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.51986	0.279597	0.061242	0.1393	83.13	15.33	0.64	6906	LP2 (2026-09-30)	PASS	NonPolyA_perM 6906 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994961	M	M	NA	Agree	0.01	4.85	0.00	15.33	6.28	20.24	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.506656	0.253859	0.062571	0.176915	79.88	18.44	0.66	2018	LP2 (2026-09-30)	PASS	NonPolyA_perM 2018 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994962	M	M	NA	Agree	0.00	4.77	0.00	18.04	6.48	21.12	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.460902	0.247643	0.059315	0.23214	73.99	24.43	0.62	1859	LP2 (2026-09-30)	PASS	NonPolyA_perM 1859 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994963	M	M	NA	Agree	0.01	5.46	0.00	17.19	6.80	23.18	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.45882	0.256426	0.05821	0.226544	74.51	23.89	0.67	1847	LP2 (2026-09-30)	PASS	NonPolyA_perM 1847 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994964	M	M	NA	Agree	0.00	3.95	0.00	13.30	5.31	17.63	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.45254	0.267485	0.054453	0.225522	74.09	23.92	0.73	7246	LP2 (2026-09-30)	PASS	NonPolyA_perM 7246 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994965	M	M	NA	Agree	0.00	3.78	0.00	14.95	6.02	18.23	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.487303	0.257719	0.054787	0.200191	76.90	21.56	0.61	7020	LP2 (2026-09-30)	PASS	NonPolyA_perM 7020 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994966	M	M	NA	Agree	0.02	5.21	0.00	16.32	6.74	21.43	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.510536	0.297943	0.058798	0.132722	82.86	14.83	0.74	8619	LP2 (2026-09-30)	PASS	NonPolyA_perM 8619 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994967	M	M	NA	Agree	0.00	5.19	0.00	18.47	7.32	22.78	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.49473	0.321056	0.065598	0.118616	83.44	14.69	0.84	4534	LP2 (2026-09-30)	PASS	NonPolyA_perM 4534 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994968	M	M	NA	Agree	0.01	4.83	0.00	17.65	6.51	22.74	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.562582	0.253647	0.058531	0.12524	84.01	14.27	0.72	7735	LP2 (2026-09-30)	PASS	NonPolyA_perM 7735 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994969	M	M	NA	Agree	0.00	5.00	0.00	17.22	7.46	22.88	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.462371	0.237744	0.06045	0.239435	73.16	25.12	0.69	1982	LP2 (2026-09-30)	PASS	NonPolyA_perM 1982 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994970	M	M	NA	Agree	0.01	5.11	0.00	18.74	8.77	26.53	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.583244	0.314155	0.062811	0.039791	91.85	5.89	0.84	7168	LP2 (2026-09-30)	PASS	NonPolyA_perM 7168 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994971	M	M	NA	Agree	0.00	5.99	0.00	20.77	8.82	26.91	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.579775	0.276489	0.060224	0.083512	88.16	10.01	0.70	6017	LP2 (2026-09-30)	PASS	NonPolyA_perM 6017 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994972	M	M	NA	Agree	0.01	5.44	0.00	18.56	8.09	24.83	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.532336	0.303359	0.06295	0.101355	86.95	11.53	0.69	8631	LP2 (2026-09-30)	PASS	NonPolyA_perM 8631 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994973	M	M	NA	Agree	0.00	6.36	0.00	22.72	8.90	30.07	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.549174	0.308264	0.058154	0.084408	88.29	9.99	0.73	5718	LP2 (2026-09-30)	PASS	NonPolyA_perM 5718 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994974	M	M	NA	Agree	0.01	5.36	0.00	18.80	7.51	26.42	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.482979	0.336712	0.053846	0.126463	84.23	14.06	0.72	6594	LP2 (2026-09-30)	PASS	NonPolyA_perM 6594 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994975	M	M	NA	Agree	0.01	5.83	0.00	22.33	7.94	25.38	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.484193	0.329511	0.06366	0.122637	83.33	14.94	0.78	4410	LP2 (2026-09-30)	PASS	NonPolyA_perM 4410 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994976	M	M	NA	Agree	0.00	4.69	0.00	15.86	5.74	21.49	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.562388	0.275702	0.064268	0.097641	87.09	11.14	0.73	8620	LP2 (2026-09-30)	PASS	NonPolyA_perM 8620 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994977	M	M	NA	Agree	0.01	4.29	0.00	15.34	6.33	22.99	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.542191	0.278686	0.060059	0.119064	84.85	13.53	0.69	6955	LP2 (2026-09-30)	PASS	NonPolyA_perM 6955 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994978	M	M	NA	Agree	0.01	4.24	0.00	16.46	6.65	22.41	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.576739	0.263627	0.053467	0.106166	85.77	12.27	0.72	6566	LP2 (2026-09-30)	PASS	NonPolyA_perM 6566 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994979	M	M	NA	Agree	0.00	5.86	0.00	20.22	7.67	29.25	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.60714	0.259095	0.059881	0.073883	89.25	9.06	0.65	5223	LP2 (2026-09-30)	PASS	NonPolyA_perM 5223 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994980	M	M	NA	Agree	0.01	5.08	0.00	19.84	7.91	27.50	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.375793	0.231964	0.073342	0.318901	65.74	33.31	0.56	1655	LP2 (2026-09-30)	PASS	NonPolyA_perM 1655 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994981	M	M	NA	Agree	0.01	4.56	0.00	16.66	6.02	20.94	NONE	RRNA_DEPLETED	0.583605	0.31611	0.067004	0.033281	91.21	6.84	0.67	6033	LP2 (2026-09-30)	PASS	NonPolyA_perM 6033 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994982	M	M	NA	Agree	0.00	5.08	0.00	18.76	7.47	26.97	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.576789	0.251547	0.075211	0.096453	87.57	11.06	0.68	2252	LP2 (2026-09-30)	PASS	NonPolyA_perM 2252 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994983	M	M	NA	Agree	0.00	6.77	0.00	25.78	9.33	27.62	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.591327	0.289159	0.067462	0.052051	92.28	6.41	0.65	1062	LP2 (2026-09-30)	PASS	NonPolyA_perM 1062 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994984	M	M	NA	Agree	0.01	3.87	0.00	13.62	6.09	19.44	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.563463	0.267776	0.068483	0.100278	87.14	11.21	0.56	1786	LP2 (2026-09-30)	PASS	NonPolyA_perM 1786 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994985	M	M	NA	Agree	0.00	5.39	0.00	20.68	7.32	26.88	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.583066	0.258508	0.075233	0.083193	88.38	9.94	0.57	1949	LP2 (2026-09-30)	PASS	NonPolyA_perM 1949 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994986	M	M	NA	Agree	0.00	5.26	0.00	21.21	7.50	28.27	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.618106	0.268513	0.061944	0.051437	91.53	6.93	0.65	5864	LP2 (2026-09-30)	PASS	NonPolyA_perM 5864 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994987	M	M	NA	Agree	0.01	5.84	0.00	23.81	9.27	31.35	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.623675	0.280064	0.061421	0.03484	92.92	5.22	0.77	5338	LP2 (2026-09-30)	PASS	NonPolyA_perM 5338 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994988	M	M	NA	Agree	0.01	6.13	0.00	19.04	7.28	26.75	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.484243	0.237986	0.068208	0.209562	76.10	22.33	0.56	1878	LP2 (2026-09-30)	PASS	NonPolyA_perM 1878 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994989	M	M	NA	Agree	0.00	6.82	0.00	24.97	10.54	35.86	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.597383	0.300257	0.084603	0.017757	95.12	3.36	0.60	1920	LP2 (2026-09-30)	PASS	NonPolyA_perM 1920 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994990	M	M	NA	Agree	0.01	4.67	0.00	17.82	6.42	21.18	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.416903	0.254195	0.081814	0.247088	72.53	26.24	0.60	3131	LP2 (2026-09-30)	PASS	NonPolyA_perM 3131 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994991	M	M	NA	Agree	0.00	7.06	0.00	27.62	10.25	33.57	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.598858	0.304535	0.073841	0.022766	94.82	3.76	0.49	1284	LP2 (2026-09-30)	PASS	NonPolyA_perM 1284 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994992	M	M	NA	Agree	0.00	6.63	0.00	22.86	9.14	28.08	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.512503	0.330096	0.097852	0.059549	90.79	7.68	0.76	2434	LP2 (2026-09-30)	PASS	NonPolyA_perM 2434 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994993	M	M	NA	Agree	0.01	6.27	0.00	22.36	8.78	28.89	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.50202	0.25469	0.0766	0.166691	80.12	18.22	0.94	1728	LP2 (2026-09-30)	PASS	NonPolyA_perM 1728 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994994	M	M	NA	Agree	0.01	7.02	0.00	23.41	9.09	31.45	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.505864	0.261964	0.072996	0.159176	80.74	17.26	0.95	1566	LP2 (2026-09-30)	PASS	NonPolyA_perM 1566 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994995	M	M	NA	Agree	0.01	7.49	0.00	24.23	9.64	29.53	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.482997	0.247693	0.069884	0.199426	77.62	20.81	0.91	1511	LP2 (2026-09-30)	PASS	NonPolyA_perM 1511 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994996	M	M	NA	Agree	0.01	9.21	0.00	24.11	10.66	33.33	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.387261	0.235261	0.06737	0.310107	66.30	32.18	0.90	1672	LP2 (2026-09-30)	PASS	NonPolyA_perM 1672 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994997	M	M	NA	Agree	0.00	7.45	0.00	27.06	10.33	33.65	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.419328	0.252082	0.072391	0.256199	71.51	26.95	0.86	1609	LP2 (2026-09-30)	PASS	NonPolyA_perM 1609 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994998	M	M	NA	Agree	0.00	6.13	0.00	18.99	7.26	21.95	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.385476	0.225813	0.068084	0.320627	64.84	33.69	0.88	1830	LP2 (2026-09-30)	PASS	NonPolyA_perM 1830 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6994999	M	M	NA	Agree	0.01	6.84	0.00	25.57	8.42	30.26	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.588635	0.3103	0.081631	0.019434	94.11	3.57	1.08	1874	LP2 (2026-09-30)	PASS	NonPolyA_perM 1874 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not