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
GSM4904088	M	M	NA	Agree	0.00	4.80	0.00	30.40	11.24	76.26	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.91781	0.042968	0.031262	0.007959	93.50	3.45	2.81	59	LP2 (2026-09-30)	PASS	NonPolyA_perM 59 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904089	M	M	NA	Agree	0.01	5.86	0.00	39.73	12.30	87.65	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.926484	0.038336	0.03046	0.00472	93.99	3.19	2.56	44	LP2 (2026-09-30)	PASS	NonPolyA_perM 44 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904090	M	M	NA	Agree	0.01	6.61	0.00	39.68	12.82	92.44	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.918694	0.044694	0.030547	0.006065	94.05	3.12	2.58	52	LP2 (2026-09-30)	PASS	NonPolyA_perM 52 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904091	M	M	NA	Agree	0.00	5.47	0.00	36.53	12.17	85.84	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.918273	0.045183	0.031074	0.00547	94.06	3.10	2.58	53	LP2 (2026-09-30)	PASS	NonPolyA_perM 53 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904092	M	M	NA	Agree	0.00	6.51	0.00	39.18	13.11	84.73	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.920259	0.044225	0.030516	0.005	93.81	3.04	2.88	46	LP2 (2026-09-30)	PASS	NonPolyA_perM 46 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904093	M	M	NA	Agree	0.02	6.67	0.00	38.96	11.09	78.21	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.92446	0.041423	0.029406	0.004711	94.30	3.06	2.41	50	LP2 (2026-09-30)	PASS	NonPolyA_perM 50 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904094	M	M	NA	Agree	0.00	6.12	0.00	40.22	12.01	81.86	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.924928	0.041232	0.029079	0.004761	94.36	3.10	2.29	51	LP2 (2026-09-30)	PASS	NonPolyA_perM 51 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904095	M	M	NA	Agree	0.01	5.48	0.00	33.78	12.61	74.60	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.917735	0.048964	0.029132	0.004169	94.51	3.03	2.20	64	LP2 (2026-09-30)	PASS	NonPolyA_perM 64 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904096	M	M	NA	Agree	0.00	6.65	0.00	40.20	11.41	82.77	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.923734	0.042816	0.02891	0.00454	93.59	3.14	3.02	64	LP2 (2026-09-30)	PASS	NonPolyA_perM 64 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904097	M	M	NA	Agree	0.01	7.54	0.00	39.10	12.05	81.49	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.91796	0.0477	0.030549	0.003791	94.00	3.05	2.68	48	LP2 (2026-09-30)	PASS	NonPolyA_perM 48 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904098	M	M	NA	Agree	0.01	5.84	0.00	32.79	10.48	72.15	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.916482	0.041744	0.029439	0.012336	93.08	4.06	2.59	55	LP2 (2026-09-30)	PASS	NonPolyA_perM 55 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904099	M	M	NA	Agree	0.02	6.50	0.00	37.98	12.05	78.09	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.911967	0.051205	0.032085	0.004744	94.03	3.29	2.41	67	LP2 (2026-09-30)	PASS	NonPolyA_perM 67 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904100	M	M	NA	Agree	0.02	5.87	0.00	36.40	10.70	74.14	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.92392	0.042315	0.028824	0.004941	94.22	3.25	2.27	49	LP2 (2026-09-30)	PASS	NonPolyA_perM 49 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904101	M	M	NA	Agree	0.00	6.49	0.00	36.68	12.11	77.99	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.914753	0.050665	0.030444	0.004138	94.07	3.04	2.63	64	LP2 (2026-09-30)	PASS	NonPolyA_perM 64 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904102	M	M	NA	Agree	0.02	6.36	0.00	36.52	11.44	81.44	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.918818	0.047378	0.029752	0.004052	94.15	2.95	2.65	65	LP2 (2026-09-30)	PASS	NonPolyA_perM 65 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904103	M	M	NA	Agree	0.00	6.64	0.00	36.52	12.32	73.86	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.919647	0.046869	0.029985	0.003499	93.49	2.85	3.43	57	LP2 (2026-09-30)	PASS	NonPolyA_perM 57 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904104	M	M	NA	Agree	0.01	6.25	0.00	34.89	12.89	76.06	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.918492	0.045991	0.03054	0.004977	93.90	3.12	2.74	58	LP2 (2026-09-30)	PASS	NonPolyA_perM 58 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904105	M	M	NA	Agree	0.00	6.44	0.00	40.88	13.48	83.03	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.915592	0.048147	0.030355	0.005905	94.02	3.16	2.59	50	LP2 (2026-09-30)	PASS	NonPolyA_perM 50 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904106	M	M	NA	Agree	0.01	6.87	0.00	37.92	13.01	75.58	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.921326	0.044108	0.029872	0.004695	94.16	2.94	2.67	58	LP2 (2026-09-30)	PASS	NonPolyA_perM 58 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904107	M	M	NA	Agree	0.01	5.49	0.00	35.42	11.92	69.98	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.921803	0.044483	0.029107	0.004607	93.52	2.99	3.23	53	LP2 (2026-09-30)	PASS	NonPolyA_perM 53 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does