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 (2026-10-22) 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
GSM9038839	M	M	NA	Agree	0.00	3.88	0.00	35.38	5.18	49.67	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.945018	0.031708	0.019264	0.00401	88.40	2.05	9.32	41	LP2 (2026-09-30)	PASS	NonPolyA_perM 41 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9038840	M	M	NA	Agree	0.00	4.27	0.00	43.57	5.63	48.55	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.947328	0.029987	0.019294	0.003391	86.22	1.95	11.63	33	LP2 (2026-09-30)	PASS	NonPolyA_perM 33 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9038841	M	M	NA	Agree	0.00	4.65	0.00	46.02	7.01	53.15	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.939756	0.03526	0.021128	0.003856	85.98	1.93	11.87	38	LP2 (2026-09-30)	PASS	NonPolyA_perM 38 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9038842	M	M	NA	Agree	0.00	3.59	0.00	32.85	6.62	47.15	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.940894	0.036182	0.018989	0.003934	86.44	1.91	11.48	41	LP2 (2026-09-30)	PASS	NonPolyA_perM 41 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9038843	M	M	NA	Agree	0.00	4.83	0.00	48.94	5.75	46.02	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.939073	0.036335	0.021359	0.003233	86.55	1.89	11.17	38	LP2 (2026-09-30)	PASS	NonPolyA_perM 38 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9038844	M	M	NA	Agree	0.00	5.41	0.00	90.37	3.68	68.45	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.929353	0.041469	0.026842	0.002336	88.02	2.21	9.37	91	LP2 (2026-09-30)	PASS	NonPolyA_perM 91 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9038845	M	M	NA	Agree	0.00	8.52	0.00	83.22	8.58	70.33	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.937772	0.038017	0.021712	0.002498	89.64	1.96	8.05	60	LP2 (2026-09-30)	PASS	NonPolyA_perM 60 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9038846	M	M	NA	Agree	0.00	5.66	0.00	55.46	6.03	54.29	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.943798	0.032723	0.020044	0.003435	88.96	1.88	8.94	30	LP2 (2026-09-30)	PASS	NonPolyA_perM 30 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9038847	M	M	NA	Agree	0.00	6.11	0.00	70.42	9.05	70.66	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.923233	0.046324	0.02755	0.002893	86.48	2.43	10.65	64	LP2 (2026-09-30)	PASS	NonPolyA_perM 64 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9038848	M	M	NA	Agree	0.00	7.56	0.00	78.32	8.40	77.26	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.927155	0.046365	0.024108	0.002372	85.48	2.17	12.04	61	LP2 (2026-09-30)	PASS	NonPolyA_perM 61 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9038849	M	M	NA	Agree	0.00	6.18	0.00	66.11	7.21	54.99	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.94128	0.034846	0.021095	0.00278	87.48	1.84	10.44	40	LP2 (2026-09-30)	PASS	NonPolyA_perM 40 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9038850	M	M	NA	Agree	0.01	5.23	0.00	45.00	9.60	56.49	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.919594	0.045953	0.031057	0.003396	85.83	2.27	11.54	75	LP2 (2026-09-30)	PASS	NonPolyA_perM 75 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9038851	M	M	NA	Agree	0.44	7.73	0.00	47.66	16.05	72.73	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.895406	0.067591	0.032728	0.004275	87.48	2.53	9.73	147	LP2 (2026-09-30)	PASS	NonPolyA_perM 147 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9038852	M	M	NA	Agree	0.01	2.48	0.00	13.44	2.86	14.76	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.891864	0.080512	0.017065	0.010559	81.01	11.14	7.12	117	LP2 (2026-09-30)	PASS	NonPolyA_perM 117 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9038853	M	M	NA	Agree	0.31	8.10	0.00	47.89	17.42	68.70	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.88902	0.074058	0.032226	0.004696	88.01	2.49	9.24	165	LP2 (2026-09-30)	PASS	NonPolyA_perM 165 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9038854	M	M	NA	Agree	0.03	8.29	0.00	47.49	13.78	65.08	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.894621	0.06846	0.033156	0.003763	87.90	2.47	9.34	112	LP2 (2026-09-30)	PASS	NonPolyA_perM 112 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9038855	M	M	NA	Agree	0.06	6.80	0.00	41.41	15.02	82.41	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.903141	0.065054	0.028372	0.003433	88.13	2.70	8.96	163	LP2 (2026-09-30)	PASS	NonPolyA_perM 163 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9038856	M	M	NA	Agree	0.82	6.08	0.00	41.72	14.29	73.85	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.905042	0.056284	0.032116	0.006558	86.18	2.74	10.77	124	LP2 (2026-09-30)	PASS	NonPolyA_perM 124 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9038857	M	M	NA	Agree	0.15	7.66	0.00	42.64	15.02	64.69	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.886786	0.071311	0.036677	0.005226	86.16	2.82	10.67	162	LP2 (2026-09-30)	PASS	NonPolyA_perM 162 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9038858	M	M	NA	Agree	0.06	4.13	0.00	28.95	6.48	52.55	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.864752	0.098644	0.027016	0.009588	86.93	3.72	9.03	207	LP2 (2026-09-30)	PASS	NonPolyA_perM 207 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does