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 (2026-10-16) 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
GSM3245009	M	M	NA	Agree	0.01	0.78	0.00	2.24	0.48	3.86	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.567404	0.050165	0.372039	0.010393	18.72	37.65	41.53	68647	LP2 (2026-09-30)	LOW_MAPPING	NonPolyA_perM 68647 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3245013	M	M	NA	Agree	0.01	0.80	0.00	1.91	0.35	3.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.495388	0.042476	0.43566	0.026475	9.71	39.90	49.00	121017	LP2 (2026-09-30)	LOW_MAPPING	NonPolyA_perM 121017 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3245014	M	M	NA	Agree	0.00	0.54	0.00	1.68	0.40	3.91	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.536399	0.038105	0.397469	0.028027	12.17	36.85	49.03	96938	LP2 (2026-09-30)	LOW_MAPPING	NonPolyA_perM 96938 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3245016	M	M	NA	Agree	0.01	0.68	0.00	2.16	0.55	3.71	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.552793	0.04428	0.37104	0.031887	14.54	34.70	48.04	79781	LP2 (2026-09-30)	LOW_MAPPING	NonPolyA_perM 79781 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3245017	M	M	NA	Agree	0.00	0.80	0.00	2.57	0.57	4.92	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.612311	0.034881	0.343772	0.009036	19.46	33.31	43.60	80304	LP2 (2026-09-30)	LOW_MAPPING	NonPolyA_perM 80304 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3245018	M	Undetermined	NA	Conflict	0.00	0.30	0.00	0.80	0.25	1.62	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.498479	0.028129	0.467542	0.00585	8.18	45.31	45.34	141808	LP2 (2026-09-30)	LOW_MAPPING	NonPolyA_perM 141808 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not