Workflow: HPC RGD paired-end workflow 2.1.2. 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
GSM8187648	not_specified	M	18.180685	Conflict	4.33	5.37	0.00	31.94	12.29	50.19	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.886914	0.074462	0.031026	0.007597	91.08	4.20	4.14	175	LP2 (2026-09-30)	PASS	NonPolyA_perM 175 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8187649	not_specified	M	20.931153	Conflict	9.67	4.55	0.00	30.02	10.56	43.08	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.887963	0.072641	0.030762	0.008634	90.57	4.03	4.81	118	LP2 (2026-09-30)	PASS	NonPolyA_perM 118 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8187650	not_specified	M	20.625000	Conflict	7.85	4.21	0.00	22.40	7.93	34.94	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.888486	0.071737	0.031998	0.007779	91.08	4.30	3.93	162	LP2 (2026-09-30)	PASS	NonPolyA_perM 162 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8187651	not_specified	M	20.830291	Conflict	11.94	3.79	0.00	28.78	10.70	40.72	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.892076	0.06908	0.030411	0.008433	91.15	4.11	4.14	112	LP2 (2026-09-30)	PASS	NonPolyA_perM 112 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8187652	not_specified	M	20.171717	Conflict	4.77	4.00	0.00	28.73	8.78	38.23	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.885411	0.075504	0.030897	0.008188	90.82	4.27	4.34	164	LP2 (2026-09-30)	PASS	NonPolyA_perM 164 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8187653	not_specified	M	20.762741	Conflict	7.24	3.82	0.00	30.16	11.21	41.44	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.891541	0.07289	0.029956	0.005613	91.41	3.80	4.20	130	LP2 (2026-09-30)	PASS	NonPolyA_perM 130 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8187654	not_specified	M	19.641414	Conflict	3.68	4.81	0.00	28.97	11.36	39.63	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.885302	0.076574	0.030063	0.008062	90.98	4.03	4.46	167	LP2 (2026-09-30)	PASS	NonPolyA_perM 167 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8187655	not_specified	M	19.002649	Conflict	8.33	5.03	0.00	30.07	11.35	42.96	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.889661	0.073776	0.030542	0.006021	91.61	3.83	3.95	133	LP2 (2026-09-30)	PASS	NonPolyA_perM 133 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8187656	not_specified	M	19.576606	Conflict	5.98	4.98	0.00	27.83	10.47	40.19	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.8884	0.071939	0.031281	0.008381	90.33	4.24	4.84	155	LP2 (2026-09-30)	PASS	NonPolyA_perM 155 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8187657	not_specified	M	20.565359	Conflict	4.73	4.57	0.00	29.28	10.64	43.08	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.888977	0.074898	0.030301	0.005823	91.27	3.80	4.39	133	LP2 (2026-09-30)	PASS	NonPolyA_perM 133 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does