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
GSM4904734	M	M	NA	Agree	0.05	6.02	0.00	38.83	7.05	65.41	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.913142	0.031806	0.048799	0.006253	83.96	8.06	7.13	73	LP2 (2026-09-30)	PASS	NonPolyA_perM 73 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904735	M	M	NA	Agree	0.00	0.89	0.00	2.53	1.91	44.20	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.906197	0.033977	0.05705	0.002775	83.81	10.34	4.69	139	LP2 (2026-09-30)	PASS	NonPolyA_perM 139 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904736	M	M	NA	Agree	0.03	4.79	0.00	31.72	7.52	76.37	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.919232	0.029849	0.047353	0.003565	86.26	8.35	4.57	134	LP2 (2026-09-30)	PASS	NonPolyA_perM 134 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904737	M	M	NA	Agree	0.03	4.61	0.00	32.09	7.63	98.73	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.868492	0.079623	0.039635	0.01225	91.23	5.43	2.94	215	LP2 (2026-09-30)	PASS	NonPolyA_perM 215 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904738	M	M	NA	Agree	0.05	7.10	0.00	45.26	11.55	109.70	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.905318	0.065684	0.027869	0.001128	94.51	2.48	2.79	125	LP2 (2026-09-30)	PASS	NonPolyA_perM 125 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904739	M	M	NA	Agree	0.10	5.13	0.00	29.47	9.33	91.86	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.889156	0.073263	0.033255	0.004326	93.37	3.77	2.56	184	LP2 (2026-09-30)	PASS	NonPolyA_perM 184 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904740	M	M	NA	Agree	0.04	6.09	0.00	32.38	8.73	105.82	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.898471	0.061493	0.030923	0.009113	93.46	4.15	2.14	182	LP2 (2026-09-30)	PASS	NonPolyA_perM 182 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904741	M	M	NA	Agree	0.01	0.39	0.00	1.74	0.76	4.99	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.224326	0.052861	0.013273	0.70954	26.15	71.24	2.38	871	LP2 (2026-09-30)	LOW_MAPPING	NonPolyA_perM 871 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4904742	M	M	NA	Agree	0.01	4.18	0.00	23.47	9.41	89.74	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.895305	0.058564	0.035418	0.010712	92.61	4.40	2.78	170	LP2 (2026-09-30)	PASS	NonPolyA_perM 170 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904743	M	M	NA	Agree	0.10	7.46	0.00	41.22	16.97	59.42	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.854539	0.103332	0.037751	0.004379	89.55	6.77	3.29	185	LP2 (2026-09-30)	PASS	NonPolyA_perM 185 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904744	M	M	NA	Agree	0.09	6.82	0.00	37.32	16.27	52.68	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.854867	0.099259	0.037395	0.008479	90.25	6.90	2.51	173	LP2 (2026-09-30)	PASS	NonPolyA_perM 173 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4904745	M	M	NA	Agree	0.10	5.07	0.00	28.72	13.90	37.98	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.849938	0.102472	0.033882	0.013709	87.43	8.52	3.63	197	LP2 (2026-09-30)	PASS	NonPolyA_perM 197 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does