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
GSM9651589	M	M	37.743105	Agree	0.13	8.03	0.00	45.38	15.44	72.78	NONE	POLYA	0.860996	0.077801	0.045852	0.015351	77.80	2.46	19.59	71	LP2 (2026-09-30)	PASS	NonPolyA_perM 71 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651590	F	F	101.337662	Agree	111.94	0.17	0.00	0.50	0.04	0.72	NONE	POLYA	0.878213	0.066983	0.045159	0.009645	77.95	1.95	19.95	59	LP2 (2026-09-30)	PASS	NonPolyA_perM 59 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651591	F	F	119.546184	Agree	61.19	0.00	0.00	0.00	0.00	0.00	NONE	POLYA	0.904667	0.041026	0.043009	0.011298	78.40	2.22	19.22	47	LP2 (2026-09-30)	PASS	NonPolyA_perM 47 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651592	M	M	34.304550	Agree	0.85	9.43	0.00	50.28	19.48	67.41	NONE	POLYA	0.837233	0.102043	0.049065	0.011659	78.45	2.08	19.29	89	LP2 (2026-09-30)	PASS	NonPolyA_perM 89 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651593	M	M	36.872561	Agree	0.04	8.99	0.00	51.16	18.22	69.89	NONE	POLYA	0.842922	0.097667	0.04858	0.010831	77.68	2.03	20.11	79	LP2 (2026-09-30)	PASS	NonPolyA_perM 79 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651594	M	M	31.403768	Agree	0.05	9.00	0.00	42.81	15.69	49.82	NONE	POLYA	0.838211	0.094032	0.050314	0.017443	78.14	2.56	19.12	80	LP2 (2026-09-30)	PASS	NonPolyA_perM 80 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651595	M	M	29.188481	Agree	0.05	10.71	0.00	50.38	18.55	71.18	NONE	POLYA	0.798863	0.128466	0.051958	0.020713	78.38	2.87	18.54	110	LP2 (2026-09-30)	PASS	NonPolyA_perM 110 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651596	F	F	102.707920	Agree	93.92	0.00	0.00	0.00	0.04	0.00	NONE	POLYA	0.87422	0.066867	0.047283	0.011631	77.39	2.07	20.39	54	LP2 (2026-09-30)	PASS	NonPolyA_perM 54 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651597	F	F	102.741935	Agree	143.55	0.00	0.00	0.00	0.00	0.00	NONE	POLYA	0.843728	0.091929	0.048923	0.015419	79.13	2.46	18.22	81	LP2 (2026-09-30)	PASS	NonPolyA_perM 81 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651598	M	M	36.606701	Agree	0.26	8.30	0.00	50.69	15.93	74.02	NONE	POLYA	0.843644	0.0898	0.048521	0.018035	76.26	2.55	21.01	74	LP2 (2026-09-30)	PASS	NonPolyA_perM 74 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651599	F	F	107.045081	Agree	132.82	0.02	0.00	0.00	0.00	0.13	NONE	POLYA	0.834347	0.097484	0.047874	0.020295	75.38	2.69	21.75	83	LP2 (2026-09-30)	PASS	NonPolyA_perM 83 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651600	F	F	94.569306	Agree	167.50	0.00	0.00	0.00	0.00	0.06	NONE	POLYA	0.821016	0.111755	0.049836	0.017393	78.74	2.56	18.50	88	LP2 (2026-09-30)	PASS	NonPolyA_perM 88 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651601	M	M	29.707756	Agree	0.06	10.97	0.00	55.75	20.14	71.06	NONE	POLYA	0.823248	0.113565	0.05359	0.009596	77.92	1.88	19.99	92	LP2 (2026-09-30)	PASS	NonPolyA_perM 92 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651602	M	M	30.693522	Agree	0.05	10.29	0.00	53.81	21.40	70.84	NONE	POLYA	0.834427	0.104003	0.050155	0.011415	79.38	2.13	18.30	86	LP2 (2026-09-30)	PASS	NonPolyA_perM 86 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651603	F	F	100.666666	Agree	197.64	0.00	0.00	0.11	0.00	0.00	NONE	POLYA	0.828868	0.114524	0.048445	0.008164	79.25	1.77	18.79	103	LP2 (2026-09-30)	PASS	NonPolyA_perM 103 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651604	M	M	32.494699	Agree	0.28	10.66	0.00	51.57	21.21	67.73	NONE	POLYA	0.8173	0.124052	0.050704	0.007944	77.74	1.74	20.31	109	LP2 (2026-09-30)	PASS	NonPolyA_perM 109 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651605	F	F	95.010695	Agree	243.27	0.00	0.00	0.00	0.00	0.00	NONE	POLYA	0.800018	0.138272	0.053589	0.008121	76.91	1.74	21.13	129	LP2 (2026-09-30)	PASS	NonPolyA_perM 129 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651606	M	M	34.757480	Agree	0.08	11.16	0.00	55.84	19.26	74.84	NONE	POLYA	0.821985	0.117588	0.049015	0.011412	77.66	2.07	20.07	98	LP2 (2026-09-30)	PASS	NonPolyA_perM 98 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651607	M	M	34.292913	Agree	0.04	10.68	0.00	53.64	19.80	74.99	NONE	POLYA	0.818646	0.125917	0.049544	0.005893	80.24	1.70	17.85	102	LP2 (2026-09-30)	PASS	NonPolyA_perM 102 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651608	M	M	34.955108	Agree	0.07	9.87	0.00	55.56	19.83	74.12	NONE	POLYA	0.820834	0.118843	0.051581	0.008742	75.62	1.82	22.35	109	LP2 (2026-09-30)	PASS	NonPolyA_perM 109 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651609	F	F	97.373873	Agree	165.31	0.00	0.00	0.07	0.00	0.05	NONE	POLYA	0.829329	0.112912	0.047284	0.010475	87.48	2.18	10.13	92	LP2 (2026-09-30)	PASS	NonPolyA_perM 92 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651610	M	M	33.319148	Agree	0.02	9.22	0.00	41.43	16.49	58.38	NONE	POLYA	0.832529	0.108373	0.051362	0.007736	75.57	1.70	22.55	91	LP2 (2026-09-30)	PASS	NonPolyA_perM 91 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651611	M	M	34.619335	Agree	0.06	8.79	0.00	43.23	17.87	67.10	NONE	POLYA	0.842817	0.100766	0.04914	0.007278	75.04	1.64	23.14	93	LP2 (2026-09-30)	PASS	NonPolyA_perM 93 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651612	F	F	91.412037	Agree	227.63	0.00	0.00	0.00	0.00	0.18	NONE	POLYA	0.799278	0.136063	0.051107	0.013551	74.16	2.11	23.53	117	LP2 (2026-09-30)	PASS	NonPolyA_perM 117 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651613	M	M	33.076045	Agree	6.05	8.94	0.00	48.46	18.78	64.70	NONE	POLYA	0.808146	0.134671	0.051404	0.005779	77.70	1.59	20.50	127	LP2 (2026-09-30)	PASS	NonPolyA_perM 127 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651614	M	M	32.344574	Agree	0.04	10.30	0.00	59.01	19.37	73.57	NONE	POLYA	0.818245	0.122554	0.050749	0.008452	77.99	1.85	19.95	116	LP2 (2026-09-30)	PASS	NonPolyA_perM 116 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651615	M	M	33.174351	Agree	0.14	10.44	0.00	52.21	20.87	68.50	NONE	POLYA	0.813175	0.128719	0.049325	0.008781	77.75	1.79	20.26	114	LP2 (2026-09-30)	PASS	NonPolyA_perM 114 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651616	F	F	85.945945	Agree	241.05	0.00	0.00	0.02	0.07	0.26	NONE	POLYA	0.800608	0.137558	0.053335	0.0085	76.57	1.85	21.36	121	LP2 (2026-09-30)	PASS	NonPolyA_perM 121 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651617	M	F	97.845238	Conflict	160.11	0.00	0.00	0.00	0.00	0.00	NONE	POLYA	0.820615	0.120153	0.051277	0.007956	80.01	1.87	17.90	105	LP2 (2026-09-30)	PASS	NonPolyA_perM 105 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651618	F	M	32.921985	Conflict	0.11	10.12	0.00	55.36	18.72	70.31	NONE	POLYA	0.816395	0.123208	0.051154	0.009244	78.10	1.91	19.78	110	LP2 (2026-09-30)	PASS	NonPolyA_perM 110 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651619	F	F	85.254385	Agree	192.26	0.00	0.00	0.13	0.00	0.10	NONE	POLYA	0.832045	0.10894	0.050015	0.009	80.82	1.98	17.00	97	LP2 (2026-09-30)	PASS	NonPolyA_perM 97 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651620	F	F	90.265217	Agree	148.34	0.00	0.00	0.03	0.04	0.20	NONE	POLYA	0.844914	0.092826	0.048059	0.014201	77.72	2.24	19.86	88	LP2 (2026-09-30)	PASS	NonPolyA_perM 88 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651621	F	F	103.521929	Agree	116.48	0.02	0.00	0.09	0.00	0.00	NONE	POLYA	0.855649	0.084575	0.049984	0.009793	77.56	1.97	20.29	74	LP2 (2026-09-30)	PASS	NonPolyA_perM 74 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651622	F	F	93.270000	Agree	131.56	0.01	0.00	0.13	0.03	0.15	NONE	POLYA	0.857494	0.086189	0.047517	0.0088	79.23	1.88	18.72	78	LP2 (2026-09-30)	PASS	NonPolyA_perM 78 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651623	M	M	33.860182	Agree	0.06	9.45	0.00	47.34	17.18	66.25	NONE	POLYA	0.839819	0.100499	0.04884	0.010842	79.90	2.13	17.77	83	LP2 (2026-09-30)	PASS	NonPolyA_perM 83 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651624	M	F	108.662790	Conflict	129.65	0.00	0.00	0.03	0.05	0.00	NONE	POLYA	0.839692	0.093623	0.048534	0.018151	70.22	2.37	27.22	81	LP2 (2026-09-30)	PASS	NonPolyA_perM 81 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651625	M	M	30.966763	Agree	0.13	8.69	0.00	48.18	15.28	74.31	NONE	POLYA	0.837145	0.101283	0.051027	0.010544	78.67	2.01	19.12	91	LP2 (2026-09-30)	PASS	NonPolyA_perM 91 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651626	F	F	102.526041	Agree	114.36	0.00	0.00	0.02	0.03	0.40	NONE	POLYA	0.868736	0.078581	0.046483	0.0062	77.94	1.67	20.22	66	LP2 (2026-09-30)	PASS	NonPolyA_perM 66 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651627	M	M	38.313513	Agree	1.01	6.38	0.00	33.50	12.70	78.24	NONE	POLYA	0.899559	0.045432	0.043316	0.011693	79.27	2.18	18.43	45	LP2 (2026-09-30)	PASS	NonPolyA_perM 45 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651628	M	M	32.110504	Agree	0.03	9.10	0.00	43.64	18.06	73.47	NONE	POLYA	0.841726	0.098432	0.049895	0.009947	78.76	1.98	19.07	84	LP2 (2026-09-30)	PASS	NonPolyA_perM 84 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651629	F	F	98.920502	Agree	143.39	0.23	0.00	0.45	0.28	0.84	NONE	POLYA	0.849029	0.093951	0.048927	0.008094	78.80	1.88	19.13	80	LP2 (2026-09-30)	PASS	NonPolyA_perM 80 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651630	F	F	99.355769	Agree	147.67	0.00	0.00	0.00	0.00	0.00	NONE	POLYA	0.852235	0.091132	0.047918	0.008714	78.45	1.88	19.48	86	LP2 (2026-09-30)	PASS	NonPolyA_perM 86 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651631	M	M	33.549839	Agree	0.08	9.86	0.00	45.42	17.81	65.27	NONE	POLYA	0.850073	0.092178	0.046064	0.011686	80.12	2.15	17.55	80	LP2 (2026-09-30)	PASS	NonPolyA_perM 80 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651632	F	F	103.004000	Agree	170.51	0.09	0.00	0.06	0.00	0.00	NONE	POLYA	0.847425	0.097025	0.048516	0.007034	77.96	1.71	20.15	82	LP2 (2026-09-30)	PASS	NonPolyA_perM 82 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651633	F	F	103.622950	Agree	187.79	0.00	0.00	0.00	0.00	0.00	NONE	POLYA	0.831636	0.111147	0.048542	0.008675	76.53	1.81	21.48	101	LP2 (2026-09-30)	PASS	NonPolyA_perM 101 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651634	M	M	37.076086	Agree	1.24	7.81	0.00	37.75	13.40	76.27	NONE	POLYA	0.84018	0.07175	0.044071	0.044	74.76	4.61	20.46	63	LP2 (2026-09-30)	PASS	NonPolyA_perM 63 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651635	M	M	30.642969	Agree	0.07	9.22	0.00	49.82	20.09	73.97	NONE	POLYA	0.840737	0.100211	0.049793	0.009259	76.70	1.95	21.16	82	LP2 (2026-09-30)	PASS	NonPolyA_perM 82 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651636	F	F	94.770731	Agree	153.83	0.08	0.00	0.10	0.04	0.33	NONE	POLYA	0.834857	0.102906	0.051024	0.011213	75.99	2.07	21.75	86	LP2 (2026-09-30)	PASS	NonPolyA_perM 86 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651637	F	F	113.628140	Agree	97.12	0.00	0.00	0.04	0.09	0.00	NONE	POLYA	0.860616	0.071256	0.047292	0.020836	78.41	2.97	18.46	64	LP2 (2026-09-30)	PASS	NonPolyA_perM 64 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651638	M	M	35.086183	Agree	0.62	8.88	0.00	43.66	15.13	74.15	NONE	POLYA	0.878427	0.068901	0.046586	0.006086	81.71	1.74	16.39	60	LP2 (2026-09-30)	PASS	NonPolyA_perM 60 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651639	M	M	32.047385	Agree	0.11	11.08	0.00	44.97	18.80	68.89	NONE	POLYA	0.846274	0.091543	0.049245	0.012937	77.95	2.21	19.67	78	LP2 (2026-09-30)	PASS	NonPolyA_perM 78 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651640	M	M	40.583643	Agree	8.65	6.27	0.00	33.42	10.97	64.04	NONE	POLYA	0.893402	0.05238	0.043114	0.011105	81.03	2.24	16.58	47	LP2 (2026-09-30)	PASS	NonPolyA_perM 47 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651641	M	M	31.682110	Agree	0.07	8.88	0.00	52.27	18.79	72.17	NONE	POLYA	0.853027	0.08923	0.04797	0.009773	78.87	1.94	19.02	78	LP2 (2026-09-30)	PASS	NonPolyA_perM 78 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9651642	F	F	96.966804	Agree	153.93	0.00	0.00	0.03	0.08	0.09	NONE	POLYA	0.838223	0.10094	0.049754	0.011084	78.03	2.05	19.73	91	LP2 (2026-09-30)	PASS	NonPolyA_perM 91 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does