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
GSM3588967	M	F	NA	Conflict	97.90	0.01	0.00	0.42	0.07	0.49	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.875378	0.058537	0.043942	0.022144	94.33	4.29	1.18	75	LP2 (2026-09-30)	PASS	NonPolyA_perM 75 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3588968	M	M	NA	Agree	0.22	8.32	0.00	45.65	17.67	115.06	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.888043	0.05309	0.050951	0.007917	95.39	3.18	1.25	85	LP2 (2026-09-30)	PASS	NonPolyA_perM 85 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3588969	M	M	NA	Agree	0.00	7.35	0.00	39.81	16.27	76.76	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.872183	0.075445	0.04501	0.007361	95.21	2.75	1.84	84	LP2 (2026-09-30)	PASS	NonPolyA_perM 84 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3588970	M	M	NA	Agree	0.04	7.62	0.00	42.82	19.46	80.12	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.835755	0.113086	0.046143	0.005016	95.86	2.37	1.53	114	LP2 (2026-09-30)	PASS	NonPolyA_perM 114 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3588971	M	M	NA	Agree	0.01	8.00	0.00	52.63	21.07	88.60	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.844612	0.101509	0.047052	0.006828	95.93	2.61	1.22	108	LP2 (2026-09-30)	PASS	NonPolyA_perM 108 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3588972	M	M	NA	Agree	0.01	7.96	0.00	47.06	18.88	88.97	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.835796	0.110394	0.047676	0.006134	96.06	2.50	1.22	109	LP2 (2026-09-30)	PASS	NonPolyA_perM 109 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does