MultiQC Report

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

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Report generated on 2021-12-03, 10:38 based on data in: /home/matdawidziuk/microcephaly/microcephaly_cov/microcephaly_qc_final

General Statistics

Showing ¹⁹⁴/₁₉₄ rows and ²¹/₃₂ columns.

Sample Name	% GC	Ins. size	≥ 1X	≥ 5X	≥ 10X	≥ 30X	≥ 50X	Median cov	Mean cov	% Aligned	M Aligned	M Total reads	Error rate	Vars	Hom	Het	SNP	Indel	Ts/Tv	Error rate	M Non-Primary	M Reads Mapped	% Mapped	% Proper Pairs	% MapQ 0 Reads	M Total seqs	% Dups	% GC	Length	% Failed	M Seqs
S100	54%	214	99.8%	99.7%	99.5%	95.7%	82.6%	88.0X	28.7X	99.8%	136.3	136.6	0.53%	435411	256605	144030	400685	34753	2.16	0.56%	0.2	135.8	99.8%	98.7%	4.4%	136.1	3.0%	52%	100 bp	18%	10.0
S101	54%	214	99.8%	99.6%	99.4%	93.5%	76.2%	77.0X	25.0X	99.8%	119.9	120.2	0.50%	381293	220124	130645	350790	30532	2.17	0.53%	0.1	119.6	99.8%	98.6%	4.2%	119.8	3.3%	52%	100 bp	9%	10.0
S102	54%	216	99.8%	99.7%	99.5%	95.6%	81.8%	86.0X	28.2X	99.8%	137.8	138.0	0.53%	412389	238748	140364	379131	33284	2.18	0.57%	0.2	137.3	99.8%	98.8%	4.5%	137.6	3.3%	52%	100 bp	9%	10.0
S103	54%	224	99.8%	99.7%	99.5%	96.2%	84.2%	90.0X	29.5X	99.8%	145.8	146.1	0.54%	461659	265808	158722	424541	37146	2.18	0.57%	0.2	145.3	99.8%	98.8%	4.4%	145.6	3.0%	52%	100 bp	9%	10.0
S104	54%	216	99.8%	99.7%	99.5%	96.3%	85.8%	98.0X	31.4X	99.8%	155.4	155.7	0.52%	477106	280009	159030	439057	38088	2.21	0.54%	0.1	155.0	99.8%	98.8%	4.1%	155.3	2.7%	52%	100 bp	9%	10.0
S105	54%	215	99.8%	99.7%	99.5%	96.1%	83.9%	90.0X	29.7X	99.8%	141.7	142.0	0.24%	448589	260661	150777	411465	37154	2.21	0.27%	0.2	141.2	99.8%	98.6%	4.3%	141.6	3.6%	52%	100 bp	9%	10.0
S106	54%	215	99.5%	99.4%	99.2%	94.9%	79.8%	82.0X	26.9X	99.8%	124.1	124.3	0.25%	435563	254861	145148	400024	35564	2.21	0.28%	0.1	123.7	99.8%	98.6%	4.3%	124.0	3.5%	52%	100 bp	9%	10.0
S107	53%	220	99.5%	99.4%	99.3%	96.5%	85.2%	91.0X	30.0X	99.8%	141.7	142.0	0.24%	479056	276333	163093	439445	39644	2.21	0.27%	0.2	141.3	99.8%	98.8%	4.3%	141.5	3.4%	52%	100 bp	9%	10.0
S108	54%	226	99.8%	99.7%	99.6%	97.3%	88.0%	100.0X	32.7X	99.8%	160.0	160.4	0.25%	534621	309076	181401	490502	44153	2.22	0.28%	0.2	159.6	99.8%	98.7%	4.4%	159.9	3.3%	52%	100 bp	18%	10.0
S109	53%	222	99.8%	99.7%	99.5%	96.2%	84.0%	89.0X	29.3X	99.8%	137.2	137.4	0.26%	454005	261708	154778	416501	37539	2.21	0.29%	0.2	136.7	99.8%	98.6%	4.5%	136.9	3.5%	52%	100 bp	9%	10.0
S11	53%	195	99.8%	99.7%	99.6%	97.9%	90.9%	110.0X	36.6X	99.7%	183.5	184.0	0.34%	696636	414370	216813	640941	55736	2.16	0.39%	0.3	164.4	99.7%	98.9%	5.0%	164.8	5.6%	52%	100 bp	9%	10.0
S110	54%	220	99.8%	99.7%	99.6%	97.9%	91.1%	112.0X	36.9X	99.8%	175.6	176.0	0.24%	576487	333357	195358	528752	47776	2.26	0.27%	0.2	175.0	99.8%	98.6%	4.2%	175.5	3.3%	52%	100 bp	9%	10.0
S111	53%	211	99.8%	99.7%	99.4%	95.1%	80.7%	83.0X	27.1X	99.8%	127.6	127.9	0.24%	410781	237006	139846	376866	33938	2.20	0.27%	0.2	127.2	99.8%	98.6%	4.5%	127.5	3.7%	52%	100 bp	9%	10.0
S112	53%	225	99.8%	99.7%	99.5%	96.4%	85.4%	93.0X	30.8X	99.8%	152.4	152.7	0.35%	461260	264811	158846	423685	37605	2.22	0.39%	0.2	151.9	99.8%	98.8%	4.2%	152.2	3.3%	51%	100 bp	9%	10.0
S113	53%	218	99.8%	99.6%	99.4%	94.7%	79.4%	81.0X	26.4X	99.8%	128.3	128.6	0.36%	436618	254096	147374	401496	35151	2.20	0.39%	0.2	127.8	99.8%	98.6%	4.4%	128.1	3.4%	52%	100 bp	9%	10.0
S114	53%	224	99.5%	99.4%	99.3%	97.1%	88.4%	99.0X	32.7X	99.8%	163.2	163.6	0.37%	509473	293486	174631	468140	41365	2.24	0.41%	0.2	162.7	99.8%	98.7%	4.4%	163.1	3.4%	51%	100 bp	9%	10.0
S115	53%	219	99.8%	99.7%	99.5%	96.5%	85.6%	93.0X	30.6X	99.8%	145.4	145.7	0.29%	419319	241135	143899	385050	34303	2.21	0.32%	0.2	145.0	99.8%	98.7%	4.2%	145.2	3.5%	52%	100 bp	9%	10.0
S116	53%	221	99.5%	99.4%	99.3%	97.7%	91.3%	110.0X	36.2X	99.8%	175.9	176.3	0.28%	487789	281598	166107	447723	40105	2.23	0.31%	0.2	175.4	99.8%	98.7%	4.1%	175.8	3.4%	52%	100 bp	9%	10.0
S117	53%	217	99.5%	99.5%	99.3%	97.7%	91.1%	110.0X	36.2X	99.8%	177.5	177.8	0.28%	478679	275251	163896	439166	39546	2.23	0.31%	0.2	176.9	99.8%	98.7%	4.3%	177.2	3.6%	52%	100 bp	9%	10.0
S118	53%	220	99.6%	99.5%	99.3%	97.8%	91.4%	110.0X	36.3X	99.8%	170.6	170.9	0.31%	521064	302258	176777	479057	42040	2.21	0.34%	0.2	170.1	99.8%	98.7%	4.2%	170.5	3.3%	52%	100 bp	9%	10.0
S119	53%	216	99.8%	99.7%	99.5%	97.2%	89.0%	103.0X	34.0X	99.8%	153.0	153.3	0.30%	479603	280752	160106	440882	38741	2.20	0.32%	0.2	152.6	99.8%	98.8%	4.4%	152.8	3.1%	52%	100 bp	9%	10.0
S12	53%	196	99.6%	99.5%	99.5%	99.0%	96.8%	150.0X	50.3X	99.8%	278.5	279.2	0.30%	948985	553347	316264	870668	78358	2.16	0.36%	0.4	250.3	99.8%	98.9%	4.8%	250.8	5.7%	52%	100 bp	9%	10.0
S120	54%	213	99.5%	99.4%	99.3%	97.0%	88.0%	99.0X	32.6X	99.8%	152.6	152.9	0.29%	458834	268260	152962	421243	37624	2.22	0.32%	0.2	152.1	99.8%	98.7%	4.2%	152.4	3.3%	52%	100 bp	9%	10.0
S121	54%	220	99.8%	99.7%	99.4%	95.5%	82.1%	87.0X	28.5X	99.8%	134.2	134.4	0.29%	405964	233036	139808	372871	33134	2.23	0.32%	0.1	133.7	99.8%	98.8%	4.3%	134.0	3.5%	52%	100 bp	9%	10.0
S122	54%	222	99.8%	99.7%	99.5%	96.6%	85.7%	94.0X	31.1X	99.8%	149.7	150.0	0.29%	433216	247482	150499	397990	35260	2.22	0.32%	0.2	149.3	99.8%	98.7%	4.2%	149.5	3.3%	52%	100 bp	9%	10.0
S123	54%	222	99.8%	99.7%	99.5%	97.3%	89.2%	106.0X	34.5X	99.8%	159.0	159.3	0.29%	519539	298474	179187	477683	41885	2.22	0.31%	0.2	158.5	99.8%	98.9%	4.2%	158.8	3.1%	52%	100 bp	9%	10.0
S124	53%	216	99.5%	99.4%	99.3%	97.8%	92.5%	115.0X	38.3X	99.8%	199.7	200.0	0.25%	573346	327457	198302	525782	47604	2.25	0.29%	0.2	199.2	99.8%	98.7%	4.4%	199.5	3.7%	51%	100 bp	9%	10.0
S125	52%	217	99.5%	99.5%	99.3%	98.1%	93.9%	121.0X	40.7X	99.8%	237.4	237.8	0.24%	585189	334587	201137	535749	49480	2.23	0.28%	0.3	236.6	99.8%	98.2%	4.5%	237.0	3.7%	51%	100 bp	9%	10.0
S126	53%	219	99.5%	99.5%	99.3%	97.3%	89.7%	103.0X	34.6X	99.8%	178.4	178.7	0.25%	516838	293336	180322	473673	43202	2.24	0.28%	0.2	177.9	99.8%	98.5%	4.4%	178.2	3.8%	51%	100 bp	9%	10.0
S127	53%	220	99.8%	99.7%	99.5%	97.1%	88.8%	101.0X	33.7X	99.8%	175.5	175.8	0.26%	513538	293312	177254	470590	42994	2.28	0.30%	0.2	174.9	99.8%	98.3%	4.5%	175.2	3.9%	51%	100 bp	18%	10.0
S128	53%	217	99.5%	99.4%	99.2%	95.1%	80.4%	80.0X	26.7X	99.8%	140.1	140.4	0.25%	400591	225237	141793	367047	33565	2.25	0.29%	0.2	139.7	99.8%	98.6%	4.5%	140.0	4.3%	51%	100 bp	9%	10.0
S129	52%	212	99.8%	99.7%	99.5%	97.7%	91.7%	109.0X	36.9X	99.8%	192.2	192.5	0.25%	555215	318803	189086	507919	47343	2.20	0.29%	0.2	191.6	99.8%	98.5%	4.5%	191.9	3.7%	50%	100 bp	9%	10.0
S130	53%	222	99.8%	99.7%	99.6%	98.6%	95.1%	134.0X	44.8X	99.8%	257.0	257.5	0.24%	706755	397125	249841	646998	59795	2.26	0.29%	0.3	256.2	99.8%	98.7%	4.6%	256.7	3.7%	51%	100 bp	9%	10.0
S131	53%	217	99.5%	99.4%	99.2%	96.4%	85.9%	92.0X	30.7X	99.8%	159.9	160.2	0.25%	475120	271779	163792	435589	39565	2.24	0.29%	0.2	159.4	99.8%	98.7%	4.4%	159.7	4.0%	51%	100 bp	9%	10.0
S132	53%	222	99.8%	99.7%	99.5%	96.9%	87.1%	95.0X	31.9X	99.8%	168.6	168.9	0.26%	501612	286986	172657	459672	41963	2.25	0.29%	0.2	168.1	99.8%	98.3%	4.6%	168.4	3.8%	51%	100 bp	9%	10.0
S133	53%	214	99.5%	99.4%	99.3%	97.7%	91.5%	110.0X	36.9X	99.8%	200.5	200.9	0.25%	540135	306853	188114	494990	45170	2.24	0.29%	0.2	199.9	99.8%	98.3%	4.5%	200.3	4.0%	51%	100 bp	9%	10.0
S134	53%	225	99.5%	99.4%	99.3%	97.6%	90.6%	104.0X	34.8X	99.8%	183.5	183.8	0.25%	557271	316459	193788	510267	47045	2.25	0.28%	0.2	183.0	99.8%	98.2%	4.4%	183.3	3.7%	51%	100 bp	9%	10.0
S135	53%	216	99.5%	99.4%	99.3%	97.2%	89.3%	101.0X	33.9X	99.8%	171.4	171.7	0.27%	504157	289238	173001	462261	41931	2.23	0.31%	0.2	170.9	99.8%	98.4%	4.5%	171.2	3.7%	51%	100 bp	9%	10.0
S136	52%	227	99.8%	99.7%	99.5%	97.5%	90.0%	102.0X	34.3X	99.8%	191.5	191.8	0.25%	537315	304212	187558	491799	45558	2.25	0.30%	0.2	190.9	99.8%	98.6%	4.4%	191.2	3.9%	51%	100 bp	9%	10.0
S137	53%	227	99.8%	99.7%	99.5%	97.1%	87.7%	96.0X	32.0X	99.8%	183.2	183.5	0.26%	528708	298760	185404	484183	44571	2.25	0.30%	0.2	182.6	99.8%	98.7%	4.5%	182.9	4.0%	51%	100 bp	18%	10.0
S138	53%	217	99.6%	99.4%	99.3%	97.4%	89.8%	103.0X	34.4X	99.8%	198.1	198.5	0.25%	525893	297362	184024	481405	44517	2.25	0.30%	0.2	197.6	99.8%	98.7%	4.5%	197.9	4.2%	51%	100 bp	9%	10.0
S139	53%	215	99.8%	99.7%	99.5%	96.9%	87.7%	97.0X	32.4X	99.8%	176.8	177.1	0.24%	486773	278696	167078	445793	41011	2.24	0.28%	0.2	176.2	99.8%	98.8%	4.4%	176.5	4.2%	51%	100 bp	9%	10.0
S140	53%	221	99.8%	99.7%	99.6%	98.5%	94.6%	127.0X	42.7X	99.8%	251.7	252.2	0.25%	641756	360674	226328	587038	54765	2.25	0.30%	0.3	250.9	99.8%	98.4%	4.4%	251.4	4.0%	51%	100 bp	18%	10.0
S141	53%	226	99.6%	99.5%	99.4%	99.0%	97.8%	186.0X	61.9X	99.9%	347.8	348.2	0.22%	937004	520464	337997	858505	78562	2.23	0.26%	0.4	346.6	99.9%	98.9%	4.3%	347.0	3.3%	51%	100 bp	18%	10.0
S142	53%	223	99.8%	99.6%	99.4%	96.8%	87.8%	101.0X	33.2X	99.9%	169.0	169.2	0.23%	514053	299945	172317	472287	41805	2.23	0.25%	0.2	168.5	99.9%	99.0%	4.2%	168.7	3.5%	51%	100 bp	9%	10.0
S143	53%	226	99.8%	99.7%	99.6%	98.6%	95.5%	141.0X	46.6X	99.9%	254.3	254.6	0.23%	671707	384336	231814	616177	55569	2.24	0.27%	0.3	253.4	99.9%	98.9%	4.3%	253.8	3.5%	51%	100 bp	0%	10.0
S144	53%	226	99.8%	99.7%	99.6%	98.1%	93.0%	120.0X	39.9X	99.9%	207.7	208.0	0.23%	611607	352532	208473	561028	50620	2.23	0.26%	0.2	207.0	99.9%	98.7%	4.3%	207.3	3.4%	51%	100 bp	9%	10.0
S145	53%	229	99.6%	99.5%	99.3%	98.1%	93.9%	125.0X	41.5X	99.9%	219.0	219.3	0.22%	622764	358703	212501	571227	51582	2.24	0.25%	0.3	218.4	99.9%	98.6%	4.3%	218.7	3.4%	51%	100 bp	0%	10.0
S146	53%	225	99.8%	99.7%	99.5%	97.6%	90.9%	110.0X	36.3X	99.8%	190.2	190.4	0.25%	565831	328631	190978	519625	46241	2.23	0.28%	0.2	189.6	99.8%	98.2%	4.2%	189.9	3.6%	51%	100 bp	9%	10.0
S147	53%	225	99.5%	99.5%	99.4%	98.3%	94.9%	134.0X	44.5X	99.9%	232.1	232.4	0.23%	664453	381096	227965	609089	55407	2.24	0.26%	0.3	231.4	99.9%	98.9%	4.4%	231.7	3.5%	51%	100 bp	0%	10.0
S148	53%	216	99.5%	99.4%	99.1%	93.2%	75.0%	73.0X	24.2X	99.8%	109.6	109.8	0.25%	426380	249982	141833	391839	34566	2.21	0.28%	0.1	109.3	99.8%	98.7%	4.3%	109.5	3.5%	51%	100 bp	9%	10.0
S149	53%	215	99.5%	99.4%	99.2%	95.8%	83.4%	87.0X	28.7X	99.8%	146.5	146.8	0.24%	468623	275036	155310	430360	38293	2.21	0.28%	0.2	146.0	99.8%	98.8%	4.3%	146.3	3.7%	51%	100 bp	9%	10.0
S150	53%	219	99.5%	99.4%	99.3%	97.3%	90.0%	107.0X	35.3X	99.8%	165.3	165.7	0.27%	581858	340347	194500	534875	47015	2.23	0.30%	0.2	164.8	99.8%	99.0%	4.3%	165.1	3.2%	51%	100 bp	9%	10.0
S151	53%	219	99.5%	99.4%	99.1%	94.8%	79.7%	80.0X	26.7X	99.8%	121.1	121.3	0.25%	465283	274506	153302	427831	37476	2.22	0.27%	0.1	120.7	99.8%	99.0%	4.2%	120.9	3.4%	51%	100 bp	9%	10.0
S152	53%	221	99.8%	99.7%	99.5%	96.9%	87.9%	99.0X	32.6X	99.8%	153.4	153.7	0.25%	538602	316913	178069	495002	43635	2.21	0.28%	0.2	152.9	99.8%	98.9%	4.1%	153.2	3.3%	51%	100 bp	9%	10.0
S153	53%	222	99.8%	99.7%	99.5%	97.5%	90.5%	109.0X	35.9X	99.8%	172.1	172.5	0.24%	594773	348179	198056	546254	48559	2.24	0.27%	0.2	171.5	99.8%	98.9%	4.3%	171.9	3.3%	51%	100 bp	18%	10.0
S154	53%	219	99.5%	99.4%	99.3%	97.1%	88.7%	100.0X	33.0X	99.8%	153.9	154.2	0.25%	535170	309939	181416	491372	43842	2.23	0.28%	0.2	153.4	99.8%	99.0%	4.2%	153.7	3.4%	51%	100 bp	0%	10.0
S155	53%	219	99.5%	99.4%	99.2%	96.9%	88.3%	99.0X	32.6X	99.8%	153.5	153.8	0.25%	533027	312359	177336	489718	43343	2.23	0.28%	0.2	153.1	99.8%	98.9%	4.2%	153.4	3.3%	51%	100 bp	9%	10.0
S156	53%	224	99.8%	99.6%	99.4%	96.0%	84.2%	88.0X	29.2X	99.9%	139.1	139.3	0.24%	478981	280062	159401	439478	39536	2.20	0.27%	0.2	138.6	99.9%	98.7%	4.3%	138.9	3.4%	51%	100 bp	9%	10.0
S157	53%	228	99.8%	99.7%	99.5%	97.6%	91.9%	117.0X	38.4X	99.9%	197.2	197.5	0.23%	597434	347845	200287	548157	49316	2.23	0.26%	0.2	196.6	99.9%	98.9%	4.2%	196.9	3.4%	51%	100 bp	9%	10.0
S158	53%	234	99.8%	99.6%	99.4%	95.8%	83.2%	86.0X	28.7X	99.8%	137.8	138.0	0.26%	489218	282608	166273	448908	40347	2.22	0.29%	0.1	137.3	99.8%	98.7%	4.3%	137.5	3.3%	51%	100 bp	0%	10.0
S159	52%	224	99.5%	99.4%	99.3%	97.6%	91.4%	105.0X	35.6X	99.9%	174.2	174.4	0.22%	570950	331921	191130	523065	47922	2.21	0.26%	0.2	173.7	99.9%	99.0%	4.2%	173.9	3.3%	50%	100 bp	0%	10.0
S16	53%	198	99.8%	99.7%	99.7%	98.6%	94.6%	127.0X	42.5X	99.7%	228.9	229.5	0.32%	753264	437310	243881	691454	61839	2.17	0.38%	0.4	205.0	99.7%	98.9%	4.9%	205.5	5.6%	52%	100 bp	9%	10.0
S160	53%	227	99.5%	99.4%	99.2%	97.0%	88.4%	97.0X	32.4X	99.9%	158.2	158.5	0.24%	525024	302768	178743	481540	43522	2.21	0.27%	0.2	157.7	99.9%	98.8%	4.2%	158.0	3.5%	51%	100 bp	9%	10.0
S161	52%	206	99.5%	99.4%	99.2%	95.4%	82.8%	85.0X	28.1X	99.7%	135.2	135.5	0.38%	524610	316986	165621	482628	42010	2.12	0.43%	0.2	134.7	99.7%	98.3%	4.5%	135.1	3.2%	50%	100 bp	0%	10.0
S162	53%	223	99.8%	99.6%	99.3%	96.0%	85.4%	93.0X	30.4X	99.8%	146.6	146.8	0.25%	478535	280202	160089	440317	38248	2.22	0.28%	0.2	146.1	99.8%	98.8%	4.3%	146.3	3.6%	51%	100 bp	0%	10.0
S163	53%	224	99.5%	99.4%	99.2%	95.8%	83.9%	87.0X	29.1X	99.8%	135.4	135.6	0.26%	465457	271350	155814	427190	38292	2.20	0.29%	0.1	135.0	99.8%	98.7%	4.4%	135.2	3.4%	51%	100 bp	9%	10.0
S164	53%	228	99.8%	99.7%	99.5%	97.8%	91.7%	111.0X	37.2X	99.9%	181.1	181.4	0.23%	603396	349669	203758	553447	49983	2.22	0.26%	0.2	180.6	99.9%	98.7%	4.4%	180.8	3.3%	51%	100 bp	9%	10.0
S165	53%	223	99.8%	99.7%	99.5%	96.5%	85.9%	92.0X	30.8X	99.9%	144.9	145.1	0.23%	462779	268416	155925	424364	38447	2.21	0.26%	0.2	144.5	99.9%	98.9%	4.2%	144.7	3.5%	51%	100 bp	9%	10.0
S166	53%	226	99.8%	99.7%	99.5%	96.9%	87.7%	97.0X	32.6X	99.8%	154.3	154.5	0.24%	510822	298690	169825	468534	42333	2.21	0.27%	0.2	153.7	99.8%	98.7%	4.3%	154.0	3.6%	51%	100 bp	9%	10.0
S167	52%	223	99.5%	99.5%	99.3%	98.2%	94.4%	125.0X	41.9X	99.9%	210.8	211.1	0.23%	625198	361998	210863	572884	52359	2.21	0.26%	0.2	210.2	99.9%	98.9%	4.2%	210.5	3.4%	51%	100 bp	0%	10.0
S168	52%	227	99.8%	99.6%	99.4%	95.5%	82.0%	83.0X	28.0X	99.9%	128.1	128.3	0.23%	456021	265126	152800	417956	38091	2.20	0.26%	0.2	127.7	99.9%	98.8%	4.2%	127.9	3.6%	51%	100 bp	9%	10.0
S169	52%	226	99.5%	99.4%	99.2%	96.9%	88.4%	96.0X	32.5X	99.8%	153.2	153.5	0.29%	553749	322397	187269	509689	44089	1.90	0.31%	0.2	152.8	99.8%	98.5%	4.2%	153.1	3.1%	50%	100 bp	0%	10.0
S170	53%	221	99.8%	99.6%	99.4%	95.3%	81.7%	83.0X	27.7X	99.9%	130.2	130.4	0.23%	447553	261808	149079	410907	36678	2.19	0.26%	0.2	129.8	99.9%	98.8%	4.3%	130.0	3.6%	51%	100 bp	9%	10.0
S171	53%	227	99.8%	99.7%	99.5%	97.5%	90.2%	108.0X	35.5X	99.8%	184.7	185.1	0.24%	636362	359409	223717	583153	53257	2.23	0.28%	0.2	184.1	99.8%	98.6%	4.3%	184.4	3.5%	51%	100 bp	18%	10.0
S172	53%	222	99.5%	99.5%	99.3%	97.4%	89.7%	105.0X	34.8X	99.8%	178.5	178.8	0.24%	641248	371783	216076	587883	53420	2.22	0.28%	0.2	177.9	99.8%	98.8%	4.3%	178.2	3.5%	51%	100 bp	0%	10.0
S173	53%	232	99.6%	99.4%	99.2%	96.1%	84.9%	90.0X	29.7X	99.8%	153.7	154.0	0.24%	581806	335968	196855	532876	48973	2.23	0.27%	0.2	153.2	99.8%	99.0%	4.2%	153.4	3.5%	51%	100 bp	9%	10.0
S174	53%	222	99.5%	99.4%	99.3%	97.5%	90.9%	109.0X	36.1X	99.8%	190.3	190.6	0.24%	667066	383675	227563	611254	55858	2.21	0.28%	0.2	189.7	99.8%	98.9%	4.1%	190.0	3.6%	51%	100 bp	18%	10.0
S175	53%	227	99.5%	99.4%	99.1%	95.3%	82.2%	85.0X	27.9X	99.8%	138.0	138.2	0.23%	507139	293194	171458	464673	42500	2.23	0.26%	0.1	137.6	99.8%	98.8%	4.1%	137.8	3.5%	51%	100 bp	9%	10.0
S176	53%	203	99.8%	99.6%	99.4%	95.6%	84.3%	91.0X	29.7X	99.9%	141.0	141.1	0.22%	526367	313333	169852	483205	43194	2.15	0.25%	0.2	140.5	99.9%	99.0%	4.1%	140.7	3.6%	51%	100 bp	18%	10.0
S177	53%	216	99.6%	99.4%	99.2%	97.0%	89.0%	102.0X	33.8X	99.8%	169.2	169.5	0.23%	596836	349245	197986	547256	49619	2.19	0.27%	0.2	168.7	99.8%	99.0%	4.1%	168.9	3.7%	51%	100 bp	18%	10.0
S178	53%	229	99.5%	99.4%	99.2%	96.9%	88.5%	101.0X	33.2X	99.8%	164.2	164.5	0.23%	603728	351254	201736	553013	50749	2.24	0.26%	0.2	163.7	99.8%	99.0%	4.0%	163.9	3.4%	51%	100 bp	9%	10.0
S179	53%	220	99.8%	99.7%	99.5%	97.4%	90.5%	110.0X	36.1X	99.8%	180.2	180.5	0.23%	613304	356448	205403	561878	51467	2.26	0.26%	0.2	179.6	99.8%	98.9%	4.2%	179.8	3.5%	51%	100 bp	18%	10.0
S180	53%	212	99.8%	99.7%	99.4%	96.4%	87.0%	100.0X	32.5X	99.8%	162.1	162.4	0.22%	570675	338690	184905	523619	47096	2.21	0.25%	0.2	161.6	99.8%	98.9%	4.3%	161.8	3.6%	51%	100 bp	18%	10.0
S181	52%	228	99.6%	99.5%	99.4%	98.4%	95.0%	133.0X	44.2X	99.9%	231.6	231.9	0.21%	756510	427031	264972	692031	64527	2.24	0.25%	0.2	230.9	99.9%	99.0%	4.3%	231.3	3.4%	51%	100 bp	18%	10.0
S182	53%	222	99.8%	99.7%	99.5%	97.2%	89.3%	105.0X	34.8X	99.8%	173.4	173.7	0.24%	622615	361557	208680	570269	52389	2.22	0.27%	0.2	172.9	99.8%	99.0%	4.2%	173.2	3.6%	51%	100 bp	18%	10.0
S183	53%	210	99.6%	99.5%	99.4%	98.3%	94.9%	137.0X	45.5X	99.8%	234.3	234.7	0.22%	764865	438076	262173	700287	64613	2.22	0.25%	0.2	233.6	99.8%	99.0%	4.2%	234.0	3.6%	51%	100 bp	9%	10.0
S184	53%	226	99.8%	99.6%	99.3%	94.2%	78.9%	80.0X	26.3X	99.8%	130.8	131.0	0.25%	482859	279617	162574	442214	40677	2.22	0.28%	0.1	130.4	99.8%	98.9%	4.2%	130.6	3.6%	51%	100 bp	18%	10.0
S185	53%	235	99.8%	99.6%	99.4%	96.2%	85.5%	93.0X	30.9X	99.8%	155.2	155.4	0.23%	573296	330305	194399	524726	48613	2.25	0.26%	0.2	154.7	99.8%	99.0%	4.2%	154.9	3.5%	51%	100 bp	9%	10.0
S186	53%	222	99.8%	99.6%	99.1%	90.0%	68.0%	65.0X	21.2X	99.9%	104.8	105.0	0.23%	420103	245427	139651	385099	35032	2.21	0.26%	0.1	104.5	99.9%	99.1%	4.0%	104.7	3.9%	51%	100 bp	18%	10.0
S187	53%	225	99.5%	99.4%	99.0%	93.5%	76.7%	76.0X	25.0X	99.8%	120.8	121.0	0.24%	462586	268231	155671	423929	38693	2.23	0.27%	0.1	120.4	99.8%	98.9%	4.1%	120.6	3.5%	51%	100 bp	18%	10.0
S188	53%	221	99.8%	99.7%	99.5%	97.9%	92.2%	119.0X	39.3X	99.8%	200.0	200.3	0.21%	680618	393625	229815	623470	57189	2.26	0.25%	0.2	199.3	99.8%	99.0%	4.1%	199.7	3.5%	51%	100 bp	18%	10.0
S189	53%	223	99.5%	99.4%	99.2%	94.7%	81.5%	86.0X	28.1X	99.8%	135.6	135.9	0.27%	517190	299616	174987	474628	42588	2.24	0.30%	0.1	135.2	99.8%	98.8%	4.3%	135.5	3.6%	51%	100 bp	0%	10.0
S190	52%	222	99.5%	99.4%	99.2%	95.5%	82.9%	86.0X	28.7X	99.8%	138.5	138.7	0.23%	506681	292573	171668	464261	42452	2.22	0.27%	0.1	138.1	99.8%	99.0%	4.0%	138.3	3.7%	51%	100 bp	9%	10.0
S191	53%	214	99.8%	99.7%	99.6%	98.3%	93.9%	128.0X	42.6X	99.8%	223.3	223.6	0.22%	754455	435382	255696	691100	63397	2.22	0.26%	0.2	222.6	99.8%	99.0%	4.1%	222.9	3.6%	51%	100 bp	18%	10.0
S19a	53%	198	99.8%	99.7%	99.6%	97.9%	90.7%	107.0X	35.5X	99.8%	190.6	191.0	0.32%	677017	396029	216651	621835	55203	2.17	0.37%	0.3	170.6	99.8%	98.9%	5.1%	171.0	5.7%	52%	100 bp	9%	10.0
S19b	53%	208	99.6%	99.5%	99.3%	97.5%	91.9%	125.0X	39.8X	99.7%	184.5	185.0	0.39%	747344	448440	240552	689032	58345	2.09	0.41%	0.2	183.9	99.7%	98.8%	4.4%	184.4	2.9%	51%	100 bp	0%	10.0
S26	53%	196	99.6%	99.5%	99.4%	98.5%	94.5%	128.0X	42.7X	99.7%	215.0	215.6	0.32%	791372	470136	256005	727049	64359	2.15	0.37%	0.3	192.6	99.8%	98.9%	4.9%	193.1	5.6%	52%	100 bp	9%	10.0
S27	53%	198	99.6%	99.5%	99.4%	98.2%	92.7%	116.0X	38.5X	99.8%	206.1	206.5	0.29%	739128	438783	239271	678977	60183	2.17	0.34%	0.3	184.9	99.8%	99.0%	4.8%	185.3	5.6%	52%	100 bp	9%	10.0
S28	54%	198	99.8%	99.7%	99.6%	96.5%	85.0%	92.0X	30.2X	99.8%	156.8	157.2	0.32%	602519	358754	187711	554387	48157	2.14	0.36%	0.2	140.2	99.8%	98.9%	5.0%	140.5	5.7%	52%	100 bp	9%	10.0
S3	52%	202	99.8%	99.7%	99.6%	97.7%	91.4%	108.0X	36.8X	99.3%	186.8	188.1	0.21%	709876	410440	231968	652369	57536	2.21	0.26%	0.3	167.9	99.2%	98.6%	5.0%	169.2	5.9%	50%	101 bp	8%	10.1
S32	53%	198	99.6%	99.5%	99.4%	98.2%	92.7%	113.0X	38.4X	99.7%	194.6	195.1	0.33%	740153	444576	234333	679705	60483	2.14	0.39%	0.3	175.1	99.8%	98.8%	4.8%	175.5	5.6%	51%	100 bp	18%	10.0
S35a	53%	200	99.6%	99.4%	99.3%	93.5%	75.3%	75.0X	24.7X	99.8%	124.0	124.2	0.35%	520682	310852	168136	479024	41694	2.14	0.39%	0.2	123.5	99.8%	98.9%	4.5%	123.7	3.3%	52%	100 bp	0%	10.0
S35b	53%	212	99.8%	99.7%	99.5%	96.3%	85.7%	97.0X	31.3X	99.8%	142.7	143.0	0.58%	565758	341884	179476	521388	44410	2.16	0.60%	0.2	142.2	99.8%	99.0%	4.2%	142.5	2.6%	51%	100 bp	9%	10.0
S37	53%	202	99.6%	99.4%	99.2%	91.5%	70.0%	68.0X	22.5X	99.8%	114.0	114.2	0.32%	482344	288888	154811	443730	38639	2.14	0.36%	0.2	113.7	99.8%	99.1%	4.5%	113.8	3.6%	51%	100 bp	0%	10.0
S38	53%	203	99.6%	99.5%	99.3%	94.1%	76.3%	76.0X	25.2X	99.8%	130.3	130.6	0.36%	547437	325454	177725	503213	44269	2.15	0.41%	0.2	129.9	99.8%	98.8%	4.4%	130.2	3.5%	51%	100 bp	9%	10.0
S39	53%	200	99.8%	99.7%	99.4%	92.2%	73.3%	73.0X	23.9X	99.8%	135.3	135.6	0.32%	521628	316486	163867	480393	41264	2.19	0.37%	0.2	134.8	99.8%	98.9%	4.8%	135.1	3.8%	51%	100 bp	0%	10.0
S4	52%	202	99.6%	99.5%	99.4%	98.1%	94.1%	123.0X	41.9X	99.2%	200.4	201.9	0.21%	823516	487656	268304	756805	66749	2.20	0.25%	0.3	180.3	99.2%	98.6%	4.9%	181.8	5.2%	50%	100 bp	8%	10.1
S40a	53%	186	99.8%	99.7%	99.4%	92.7%	74.1%	73.0X	23.8X	99.8%	114.3	114.5	0.36%	537647	334175	161673	495878	41801	2.08	0.40%	0.2	113.8	99.8%	99.0%	4.7%	114.1	3.3%	51%	100 bp	0%	10.0
S40b	54%	215	99.5%	99.4%	99.3%	97.1%	89.1%	106.0X	34.3X	99.8%	165.5	165.7	0.24%	595662	353121	195299	548449	47253	2.09	0.26%	0.2	165.0	99.8%	98.6%	4.3%	165.3	3.2%	52%	100 bp	9%	10.0
S41	53%	184	99.8%	99.7%	99.5%	95.4%	82.2%	87.0X	28.4X	99.8%	128.4	128.7	0.36%	623775	387172	188147	575360	48454	2.09	0.39%	0.2	127.9	99.8%	99.0%	4.9%	128.2	2.9%	51%	100 bp	9%	10.0
S42	53%	177	99.6%	99.4%	99.2%	94.6%	79.8%	83.0X	27.2X	99.7%	130.4	130.8	0.41%	612494	387661	177964	565657	46860	2.04	0.46%	0.2	129.9	99.7%	98.7%	4.7%	130.3	3.3%	52%	100 bp	9%	10.0
S46	53%	181	99.6%	99.5%	99.3%	96.6%	86.3%	96.0X	31.7X	99.7%	140.5	141.0	0.42%	684327	427182	203830	631054	53294	2.05	0.45%	0.2	140.0	99.7%	98.8%	4.7%	140.4	2.8%	51%	100 bp	0%	10.0
S49	54%	177	99.8%	99.7%	99.4%	93.1%	76.2%	77.0X	24.7X	99.8%	127.7	128.0	0.35%	563782	356523	163731	520284	43526	2.05	0.40%	0.2	127.3	99.8%	98.7%	4.7%	127.6	3.8%	52%	100 bp	9%	10.0
S52	53%	199	99.6%	99.4%	99.2%	93.8%	76.2%	76.0X	25.1X	99.8%	110.9	111.2	0.38%	442536	261885	145552	407469	35088	2.21	0.41%	0.1	110.5	99.8%	99.1%	4.3%	110.8	3.2%	52%	100 bp	9%	10.0
S53	53%	201	99.8%	99.7%	99.6%	97.4%	88.3%	100.0X	33.1X	99.8%	154.1	154.5	0.37%	565326	335740	183733	519521	45846	2.23	0.42%	0.2	153.6	99.8%	99.0%	4.5%	153.9	3.0%	52%	100 bp	0%	10.0
S57	53%	198	99.8%	99.7%	99.5%	95.5%	81.4%	84.0X	27.8X	99.8%	129.3	129.6	0.35%	490055	290033	160325	450386	39696	2.20	0.39%	0.2	128.9	99.8%	98.9%	4.4%	129.2	3.6%	52%	100 bp	18%	10.0
S59	53%	204	99.6%	99.5%	99.3%	96.7%	85.9%	96.0X	31.5X	99.8%	162.1	162.4	0.25%	538333	309393	185545	494985	43382	2.17	0.28%	0.2	161.5	99.8%	98.8%	4.3%	161.8	3.3%	51%	97 bp	9%	10.0
S6	52%	198	99.6%	99.5%	99.4%	97.9%	93.4%	120.0X	40.5X	99.3%	196.9	198.3	0.21%	728405	428053	241105	670029	58411	2.20	0.24%	0.3	177.2	99.3%	98.7%	4.8%	178.5	5.6%	50%	100 bp	8%	10.1
S63	53%	198	99.6%	99.5%	99.4%	98.4%	94.2%	130.0X	42.3X	99.8%	232.1	232.5	0.23%	654896	374319	227235	601603	53338	2.20	0.26%	0.2	231.4	99.8%	99.1%	4.5%	231.8	3.2%	52%	96 bp	9%	10.0
S66	53%	210	99.5%	99.4%	99.2%	95.4%	82.0%	87.0X	28.1X	99.9%	124.6	124.8	0.28%	486658	288230	159301	447554	39127	2.16	0.30%	0.1	124.2	99.9%	99.0%	4.3%	124.3	3.0%	51%	100 bp	0%	10.0
S67	53%	204	99.8%	99.7%	99.6%	97.5%	89.3%	106.0X	34.6X	99.9%	155.7	155.9	0.26%	569807	339541	183950	523526	46318	2.16	0.29%	0.2	155.1	99.9%	99.1%	4.4%	155.3	3.2%	51%	100 bp	9%	10.0
S68	53%	214	99.8%	99.7%	99.6%	96.9%	85.9%	93.0X	31.0X	99.8%	143.9	144.2	0.51%	493779	285502	168106	453634	40181	2.22	0.55%	0.2	143.4	99.8%	99.1%	4.4%	143.6	2.8%	51%	100 bp	9%	10.0
S7	52%	210	99.8%	99.7%	99.5%	96.3%	85.7%	89.0X	30.3X	99.3%	147.4	148.5	0.22%	636459	372773	203515	585160	51325	2.21	0.26%	0.2	132.6	99.3%	98.7%	4.9%	133.6	5.5%	50%	100 bp	8%	10.1
S74	53%	212	99.8%	99.7%	99.6%	97.2%	86.9%	96.0X	32.0X	99.9%	151.6	151.8	0.43%	569063	330941	191326	522303	46804	2.21	0.47%	0.2	151.0	99.9%	99.0%	4.4%	151.2	2.9%	51%	100 bp	9%	10.0
S76	53%	203	99.5%	99.5%	99.3%	96.4%	84.3%	90.0X	29.9X	99.9%	137.0	137.2	0.47%	478042	279504	159736	439259	38821	2.21	0.50%	0.1	136.6	99.9%	99.0%	4.4%	136.8	3.1%	52%	100 bp	9%	10.0
S77	53%	205	99.5%	99.5%	99.3%	94.9%	78.9%	80.0X	26.7X	99.9%	122.9	123.0	0.44%	428945	247761	145836	393613	35364	2.22	0.48%	0.1	122.5	99.9%	99.0%	4.3%	122.7	3.3%	51%	100 bp	18%	10.0
S78	53%	208	99.8%	99.7%	99.5%	97.0%	87.8%	99.0X	32.9X	99.8%	146.0	146.3	0.35%	621664	377185	194074	571279	50423	2.06	0.38%	0.2	145.5	99.8%	99.1%	4.3%	145.8	3.0%	50%	100 bp	0%	10.0
S79	53%	211	99.6%	99.5%	99.4%	98.2%	93.1%	121.0X	39.9X	99.8%	190.3	190.7	0.36%	767420	448234	257015	705291	62183	2.10	0.39%	0.2	189.7	99.8%	99.0%	4.5%	190.1	2.9%	51%	100 bp	0%	10.0
S8	52%	204	99.8%	99.7%	99.5%	96.4%	85.5%	89.0X	30.4X	99.2%	156.1	157.3	0.22%	595938	348715	191248	548222	47748	2.21	0.26%	0.3	140.0	99.2%	98.5%	5.1%	141.2	5.5%	50%	100 bp	8%	10.1
S80	53%	215	99.8%	99.7%	99.6%	97.4%	89.0%	106.0X	34.6X	99.7%	158.8	159.2	0.43%	624241	368302	205752	574072	50204	2.15	0.46%	0.2	158.3	99.7%	99.0%	4.3%	158.7	2.7%	51%	100 bp	0%	10.0
S83	53%	237	99.8%	99.7%	99.5%	97.3%	87.6%	96.0X	32.1X	99.9%	150.4	150.6	0.28%	564998	320646	197465	518131	46905	2.20	0.31%	0.2	149.8	99.9%	99.1%	4.2%	150.1	3.0%	51%	100 bp	9%	10.0
S84	53%	235	99.5%	99.5%	99.3%	97.1%	86.8%	94.0X	31.2X	99.8%	148.6	148.9	0.27%	541454	311025	185482	496537	44945	2.18	0.29%	0.2	148.2	99.8%	99.2%	4.1%	148.4	3.0%	51%	100 bp	0%	10.0
S86	53%	231	99.8%	99.7%	99.6%	98.1%	91.7%	112.0X	37.2X	99.9%	173.8	174.1	0.27%	618236	357439	209363	566826	51451	2.19	0.29%	0.2	173.3	99.9%	99.2%	4.2%	173.6	3.0%	51%	100 bp	0%	10.0
S87	53%	236	99.5%	99.4%	99.3%	95.8%	81.4%	84.0X	27.8X	99.8%	127.4	127.6	0.28%	466953	265809	162373	428199	38782	2.23	0.30%	0.1	127.0	99.8%	99.2%	4.1%	127.2	3.1%	51%	100 bp	9%	10.0
S88	53%	226	99.5%	99.5%	99.4%	98.1%	92.2%	114.0X	37.6X	99.8%	178.6	178.9	0.29%	658212	377849	225905	603780	54476	2.19	0.32%	0.2	178.1	99.8%	99.2%	4.1%	178.4	2.8%	51%	100 bp	9%	10.0
S89	53%	222	99.5%	99.5%	99.4%	98.6%	94.9%	130.0X	43.1X	99.8%	205.7	206.0	0.26%	690278	397497	235062	632591	57742	2.18	0.29%	0.2	205.0	99.8%	99.2%	4.1%	205.4	3.1%	51%	100 bp	0%	10.0
S9	52%	198	99.8%	99.7%	99.4%	94.7%	80.2%	80.0X	27.0X	99.2%	137.3	138.3	0.21%	515609	304121	163137	474476	41162	2.19	0.25%	0.2	123.0	99.2%	98.6%	5.1%	124.0	5.9%	50%	100 bp	8%	10.1
S92	53%	223	99.5%	99.5%	99.3%	97.7%	90.3%	106.0X	35.3X	99.9%	159.0	159.2	0.25%	606030	353746	202147	555923	50148	2.16	0.28%	0.2	158.5	99.9%	99.2%	4.2%	158.6	3.0%	51%	100 bp	0%	10.0
S93	53%	232	99.8%	99.6%	99.3%	92.8%	73.3%	72.0X	23.7X	99.8%	111.5	111.7	0.26%	440716	253468	151146	404630	36123	2.16	0.28%	0.1	111.2	99.8%	98.5%	4.5%	111.4	3.4%	51%	100 bp	9%	10.0
S94	53%	230	99.5%	99.4%	99.3%	96.7%	85.7%	91.0X	30.2X	99.8%	145.6	145.9	0.25%	511651	294817	174834	469674	42003	2.16	0.28%	0.2	145.2	99.8%	98.2%	4.3%	145.5	3.5%	51%	100 bp	9%	10.0
S95	53%	225	99.8%	99.7%	99.5%	96.6%	85.7%	93.0X	30.6X	99.8%	146.0	146.3	0.26%	529450	308891	177241	486162	43328	2.14	0.29%	0.2	145.6	99.8%	98.3%	4.4%	145.9	3.2%	51%	100 bp	9%	10.0
S99	54%	213	99.8%	99.7%	99.4%	94.9%	80.8%	86.0X	27.7X	99.8%	137.7	138.0	0.53%	429093	250811	143900	394741	34380	2.18	0.56%	0.2	137.3	99.8%	98.8%	4.4%	137.5	3.2%	52%	100 bp	18%	10.0
T1	52%	199	99.6%	99.5%	99.4%	98.3%	94.8%	130.0X	43.8X	99.4%	232.7	234.2	0.21%	768292	449387	256236	706540	61799	2.21	0.25%	0.4	209.1	99.3%	98.8%	4.9%	210.5	5.7%	50%	100 bp	8%	10.1
T10	53%	198	99.6%	99.5%	99.5%	98.9%	96.6%	146.0X	48.9X	99.7%	268.2	268.9	0.31%	923609	534300	312233	847653	75990	2.16	0.37%	0.4	240.2	99.7%	98.8%	4.9%	240.9	5.7%	52%	100 bp	9%	10.0
T13	53%	198	99.8%	99.7%	99.7%	99.1%	96.8%	152.0X	50.9X	99.8%	275.0	275.7	0.31%	936546	530525	315576	859149	77438	2.17	0.37%	0.4	246.4	99.8%	98.9%	5.0%	247.0	5.6%	52%	100 bp	9%	10.0
T14	55%	188	99.8%	99.7%	99.4%	92.0%	78.0%	96.0X	27.4X	99.7%	183.9	184.4	0.32%	704396	405582	233868	649020	55408	2.17	0.38%	0.7	163.0	99.7%	98.0%	5.1%	163.4	5.2%	54%	100 bp	0%	10.0
T15	53%	199	99.6%	99.5%	99.4%	97.0%	87.1%	94.0X	31.7X	99.8%	153.0	153.4	0.32%	549950	331558	173568	505770	44207	2.14	0.36%	0.2	137.4	99.8%	99.0%	4.8%	137.8	5.7%	52%	100 bp	9%	10.0
T17	53%	197	99.8%	99.8%	99.7%	99.3%	98.1%	200.0X	65.2X	99.8%	329.2	329.8	0.30%	1064616	591071	373141	978970	85693	2.19	0.34%	0.4	294.3	99.8%	99.2%	4.9%	295.0	5.6%	52%	101 bp	9%	10.0
T18	53%	198	99.8%	99.7%	99.6%	97.9%	90.8%	107.0X	36.0X	99.8%	186.5	187.0	0.33%	652681	383418	207220	599419	53286	2.19	0.38%	0.3	167.1	99.8%	98.9%	5.1%	167.5	5.9%	52%	100 bp	9%	10.0
T2	52%	200	99.8%	99.7%	99.4%	95.0%	81.0%	81.0X	27.3X	99.5%	140.5	141.3	0.21%	527121	310554	166615	484529	42614	2.20	0.25%	0.2	125.9	99.4%	98.8%	5.1%	126.6	5.7%	50%	100 bp	8%	10.1
T20	53%	199	99.8%	99.7%	99.6%	98.1%	91.9%	112.0X	37.3X	99.7%	195.0	195.6	0.34%	697284	406371	224617	640691	56625	2.17	0.39%	0.3	174.3	99.7%	98.8%	5.0%	174.8	5.7%	52%	100 bp	9%	10.0
T21	53%	203	99.8%	99.7%	99.6%	97.9%	90.7%	108.0X	35.8X	99.8%	186.8	187.2	0.31%	701607	412099	223715	644927	56720	2.17	0.36%	0.3	167.2	99.8%	98.9%	4.9%	167.6	6.1%	52%	100 bp	9%	10.0
T22	54%	195	99.8%	99.7%	99.7%	98.9%	96.2%	158.0X	51.1X	99.8%	248.3	248.8	0.33%	914036	526943	303263	842788	71291	2.18	0.36%	0.4	222.0	99.8%	99.1%	5.0%	222.5	5.5%	52%	100 bp	0%	10.0
T23	53%	197	99.6%	99.5%	99.4%	98.2%	92.5%	115.0X	38.3X	99.8%	207.8	208.3	0.31%	775104	462689	248643	712175	62957	2.13	0.37%	0.4	186.2	99.8%	98.8%	5.0%	186.6	5.7%	52%	100 bp	9%	10.0
T24	53%	195	99.6%	99.5%	99.4%	98.6%	95.6%	144.0X	47.3X	99.8%	225.5	225.9	0.30%	829831	491855	270829	763746	66116	2.16	0.33%	0.3	201.8	99.8%	99.1%	4.9%	202.2	5.4%	52%	100 bp	9%	10.0
T25	53%	200	99.8%	99.7%	99.7%	98.7%	94.7%	129.0X	43.1X	99.7%	231.9	232.5	0.31%	824611	476513	268688	756270	68367	2.19	0.37%	0.4	207.9	99.7%	98.9%	5.0%	208.5	5.7%	52%	100 bp	9%	10.0
T29	53%	196	99.7%	99.5%	99.4%	98.3%	93.5%	121.0X	40.4X	99.8%	210.7	211.1	0.30%	740867	438181	241352	680413	60490	2.16	0.36%	0.3	189.6	99.8%	98.9%	4.9%	190.0	5.8%	52%	100 bp	18%	10.0
T30	54%	199	99.8%	99.7%	99.6%	97.5%	88.5%	102.0X	33.4X	99.8%	188.2	188.7	0.44%	648081	380006	208407	597066	51041	2.15	0.50%	0.3	168.3	99.8%	99.0%	5.1%	168.7	6.0%	53%	100 bp	9%	10.0
T31	53%	200	99.6%	99.5%	99.4%	98.6%	94.7%	128.0X	42.8X	99.8%	222.1	222.6	0.31%	790620	466065	258981	725925	64723	2.15	0.36%	0.3	198.9	99.8%	98.9%	5.0%	199.4	5.7%	52%	100 bp	9%	10.0
T33	54%	199	99.8%	99.7%	99.6%	98.3%	93.3%	124.0X	40.6X	99.6%	211.2	212.1	0.33%	763530	444436	247840	702489	61064	2.17	0.38%	0.3	188.6	99.6%	98.7%	4.8%	189.4	5.6%	52%	100 bp	9%	10.0
T34	53%	200	99.6%	99.5%	99.4%	96.9%	86.6%	95.0X	31.6X	99.8%	159.6	159.9	0.33%	656963	390610	212971	603628	53374	2.14	0.38%	0.2	159.0	99.8%	99.0%	4.7%	159.3	3.2%	51%	100 bp	9%	10.0
T36	53%	193	99.8%	99.7%	99.5%	96.0%	83.5%	90.0X	29.5X	99.8%	145.6	145.8	0.34%	621051	373448	197781	571271	49806	2.14	0.38%	0.2	145.0	99.8%	99.0%	4.6%	145.3	3.1%	52%	100 bp	9%	10.0
T43	54%	181	99.6%	99.4%	99.2%	93.9%	77.7%	79.0X	25.6X	99.7%	121.7	122.0	0.39%	575341	360236	170501	530777	44602	2.05	0.43%	0.2	121.3	99.7%	98.8%	4.8%	121.6	3.1%	52%	100 bp	0%	10.0
T44	53%	181	99.6%	99.5%	99.3%	95.2%	81.5%	85.0X	28.0X	99.6%	138.2	138.7	0.43%	549507	343345	163330	506703	42828	2.09	0.48%	0.2	137.7	99.6%	98.8%	4.5%	138.2	3.4%	52%	100 bp	9%	10.0
T45	53%	181	99.8%	99.7%	99.6%	96.7%	86.5%	97.0X	31.9X	99.8%	142.6	143.0	0.36%	708432	439477	213238	652758	55706	2.05	0.39%	0.2	142.2	99.8%	98.9%	4.6%	142.5	2.9%	51%	100 bp	9%	10.0
T47	53%	179	99.6%	99.5%	99.3%	96.7%	86.6%	97.0X	31.8X	99.7%	144.9	145.2	0.38%	676497	419224	204568	623836	52685	2.05	0.42%	0.2	144.4	99.7%	98.8%	4.6%	144.8	3.0%	52%	100 bp	0%	10.0
T48	54%	182	99.8%	99.7%	99.5%	94.2%	78.4%	80.0X	26.0X	99.6%	118.6	119.0	0.44%	611006	381271	183223	564523	46523	2.05	0.47%	0.2	118.1	99.6%	98.6%	4.9%	118.6	2.7%	52%	100 bp	9%	10.0
T5	52%	203	99.6%	99.5%	99.3%	97.2%	89.9%	102.0X	34.7X	99.2%	164.3	165.7	0.21%	709300	422596	228449	651883	57452	2.18	0.25%	0.3	148.1	99.1%	98.5%	4.8%	149.4	5.6%	50%	100 bp	17%	10.1
T50	54%	178	99.6%	99.4%	99.2%	93.3%	76.5%	78.0X	25.2X	99.8%	117.7	118.0	0.38%	572040	359776	168503	528309	43752	2.05	0.42%	0.2	117.2	99.8%	98.9%	4.7%	117.5	3.1%	52%	100 bp	0%	10.0
T51	53%	180	99.8%	99.7%	99.5%	95.6%	83.3%	88.0X	29.0X	99.8%	149.3	149.6	0.30%	614077	386357	179097	565483	48627	2.07	0.36%	0.2	148.7	99.8%	99.0%	4.7%	149.0	3.6%	51%	100 bp	0%	10.0
T54	53%	197	99.6%	99.5%	99.4%	97.1%	87.3%	96.0X	32.0X	99.7%	150.0	150.4	0.36%	513299	301136	170740	471919	41409	2.21	0.41%	0.2	149.5	99.7%	98.8%	4.5%	149.9	3.4%	52%	100 bp	0%	10.0
T55	53%	201	99.6%	99.5%	99.4%	97.1%	86.9%	94.0X	31.3X	99.7%	148.8	149.3	0.39%	546648	319383	182705	502131	44556	2.21	0.44%	0.2	148.4	99.7%	98.8%	4.6%	148.8	3.2%	52%	100 bp	0%	10.0
T56	53%	203	99.6%	99.5%	99.3%	96.6%	84.7%	90.0X	29.9X	99.7%	142.1	142.5	0.42%	512473	300983	170147	471180	41326	2.23	0.47%	0.2	141.6	99.7%	98.9%	4.5%	142.1	3.1%	52%	100 bp	0%	10.0
T58	53%	214	99.6%	99.5%	99.3%	96.8%	85.9%	93.0X	30.5X	99.8%	155.2	155.5	0.25%	502226	286024	174775	460837	41431	2.23	0.29%	0.2	154.7	99.8%	99.2%	4.2%	155.0	3.2%	51%	97 bp	0%	10.0
T60	53%	206	99.6%	99.5%	99.3%	96.2%	84.1%	92.0X	30.0X	99.8%	154.2	154.5	0.25%	508627	292996	174093	467133	41529	2.19	0.28%	0.2	153.8	99.8%	99.2%	4.2%	154.1	3.5%	52%	97 bp	9%	10.0
T61	53%	207	99.6%	99.5%	99.3%	96.4%	84.6%	92.0X	29.9X	99.8%	153.3	153.6	0.27%	555010	324501	186037	510606	44451	2.15	0.30%	0.2	152.8	99.8%	99.1%	4.4%	153.1	3.3%	51%	97 bp	9%	10.0
T62	53%	234	99.6%	99.5%	99.4%	98.4%	94.7%	139.0X	44.7X	99.8%	233.1	233.5	0.25%	684068	380773	247252	628092	56016	2.25	0.27%	0.2	232.4	99.8%	99.2%	4.2%	232.7	2.9%	52%	99 bp	9%	10.0
T64	53%	219	99.8%	99.7%	99.4%	93.4%	74.4%	73.0X	24.0X	99.9%	105.9	106.1	0.29%	456657	268854	150473	419353	37337	2.18	0.32%	0.1	105.5	99.8%	99.0%	4.3%	105.7	2.9%	51%	100 bp	9%	10.0
T65	53%	216	99.5%	99.4%	99.3%	95.3%	80.6%	83.0X	27.4X	99.8%	117.5	117.7	0.31%	470093	275440	156357	431820	38300	2.21	0.33%	0.1	117.1	99.8%	99.1%	4.3%	117.3	3.0%	51%	100 bp	0%	10.0
T69	53%	204	99.8%	99.7%	99.5%	94.9%	79.3%	81.0X	26.9X	99.8%	119.3	119.5	0.51%	440876	257799	147568	405392	35511	2.19	0.54%	0.1	118.9	99.8%	99.0%	4.4%	119.1	3.0%	51%	100 bp	9%	10.0
T70	53%	216	99.5%	99.4%	99.2%	94.7%	77.6%	76.0X	25.3X	99.9%	116.6	116.8	0.45%	418163	238414	145197	383631	34557	2.21	0.48%	0.1	116.2	99.9%	99.1%	4.3%	116.4	3.3%	51%	100 bp	0%	10.0
T71	52%	214	99.8%	99.7%	99.6%	97.9%	90.5%	104.0X	35.3X	99.8%	158.8	159.1	0.49%	553859	319807	188406	508239	45666	2.20	0.53%	0.2	158.3	99.8%	99.1%	4.3%	158.5	2.8%	51%	100 bp	0%	10.0
T72	53%	202	99.5%	99.5%	99.3%	97.0%	87.1%	96.0X	32.0X	99.8%	149.7	149.9	0.46%	494451	289905	164017	453933	40546	2.20	0.50%	0.2	149.2	99.8%	99.0%	4.4%	149.4	3.2%	51%	100 bp	0%	10.0
T73	53%	207	99.5%	99.5%	99.3%	96.6%	85.3%	92.0X	30.1X	99.9%	141.7	141.8	0.45%	489678	284979	164617	449625	40094	2.21	0.49%	0.1	141.2	99.9%	99.1%	4.3%	141.3	3.0%	52%	100 bp	0%	10.0
T75	53%	203	99.5%	99.5%	99.3%	96.1%	83.2%	88.0X	29.2X	99.9%	134.1	134.3	0.45%	484706	283170	162008	445205	39542	2.19	0.48%	0.1	133.7	99.9%	99.1%	4.4%	133.8	3.1%	52%	100 bp	9%	10.0
T81	53%	208	99.5%	99.4%	99.3%	96.4%	86.1%	98.0X	31.8X	99.8%	145.3	145.6	0.37%	538775	322969	173030	496018	42777	2.15	0.40%	0.1	144.8	99.8%	99.1%	4.2%	145.1	3.2%	51%	100 bp	0%	10.0
T82	53%	212	99.8%	99.7%	99.5%	97.2%	88.5%	106.0X	34.3X	99.7%	159.5	159.9	0.38%	598147	356209	194498	550735	47444	2.17	0.41%	0.1	159.0	99.7%	99.1%	4.2%	159.4	2.9%	51%	100 bp	0%	10.0
T85	53%	236	99.8%	99.7%	99.6%	98.1%	91.3%	111.0X	36.6X	99.8%	173.8	174.0	0.29%	595351	341562	204439	546047	49352	2.21	0.31%	0.2	173.2	99.8%	99.2%	4.1%	173.5	2.9%	51%	100 bp	0%	10.0
T90	53%	227	99.6%	99.5%	99.4%	98.5%	94.8%	130.0X	43.2X	99.9%	209.4	209.7	0.26%	698540	398790	241165	639972	58602	2.20	0.29%	0.2	208.8	99.9%	99.2%	4.1%	209.1	3.1%	51%	100 bp	0%	10.0
T91	53%	228	99.6%	99.5%	99.4%	98.6%	95.0%	129.0X	43.2X	99.9%	207.5	207.9	0.27%	720059	411344	248492	659869	60253	2.20	0.30%	0.2	206.9	99.8%	99.2%	4.1%	207.2	3.0%	51%	100 bp	9%	10.0
T96	54%	220	99.5%	99.4%	99.1%	91.6%	70.5%	69.0X	22.7X	99.8%	103.0	103.2	0.26%	408296	237890	137484	375392	32931	2.14	0.29%	0.1	102.7	99.8%	98.4%	4.5%	102.9	3.3%	52%	100 bp	9%	10.0
T97	53%	220	99.5%	99.4%	99.1%	92.1%	71.4%	69.0X	22.9X	99.8%	103.2	103.4	0.25%	406075	238586	134435	373036	33071	2.07	0.27%	0.1	102.9	99.8%	98.5%	4.3%	103.1	3.5%	51%	100 bp	9%	10.0
T98	53%	220	99.5%	99.4%	99.3%	97.8%	91.3%	111.0X	36.5X	99.8%	177.4	177.8	0.25%	632258	367803	213066	580888	51407	2.14	0.28%	0.2	176.9	99.8%	98.5%	4.4%	177.2	3.1%	51%	100 bp	9%	10.0

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Group	Column	Description	ID	Scale
\|\|	QualiMap	% GC	Mean GC content	`avg_gc`	None
\|\|	QualiMap	Ins. size	Median insert size	`median_insert_size`	None
\|\|	QualiMap	≥ 1X	Fraction of genome with at least 1X coverage	`1_x_pc`	None
\|\|	QualiMap	≥ 5X	Fraction of genome with at least 5X coverage	`5_x_pc`	None
\|\|	QualiMap	≥ 10X	Fraction of genome with at least 10X coverage	`10_x_pc`	None
\|\|	QualiMap	≥ 30X	Fraction of genome with at least 30X coverage	`30_x_pc`	None
\|\|	QualiMap	≥ 50X	Fraction of genome with at least 50X coverage	`50_x_pc`	None
\|\|	QualiMap	Median cov	Median coverage	`median_coverage`	None
\|\|	QualiMap	Mean cov	Mean coverage	`mean_coverage`	None
\|\|	QualiMap	% Aligned	% mapped reads	`percentage_aligned`	None
\|\|	QualiMap	M Aligned	Number of mapped reads (millions)	`mapped_reads`	read_count
\|\|	QualiMap	M Total reads	Number of reads (millions)	`total_reads`	read_count
\|\|	QualiMap	Error rate	Alignment error rate. Total edit distance (SAM NM field) over the number of mapped bases	`general_error_rate`	None
\|\|	Bcftools Stats	Vars	Variations total	`number_of_records`	None
\|\|	Bcftools Stats	Hom	Variations homozygous	`variations_hom`	None
\|\|	Bcftools Stats	Het	Variations heterozygous	`variations_het`	None
\|\|	Bcftools Stats	SNP	Variation SNPs	`number_of_SNPs`	None
\|\|	Bcftools Stats	Indel	Variation Insertions/Deletions	`number_of_indels`	None
\|\|	Bcftools Stats	Ts/Tv	Variant SNP transition / transversion ratio	`tstv`	None
\|\|	Bcftools Stats	MNP	Variation multinucleotide polymorphisms	`number_of_MNPs`	None
\|\|	Samtools Stats	Error rate	Error rate: mismatches (NM) / bases mapped (CIGAR)	`error_rate`	None
\|\|	Samtools Stats	M Non-Primary	Non-primary alignments (millions)	`non-primary_alignments`	read_count
\|\|	Samtools Stats	M Reads Mapped	Reads Mapped in the bam file (millions)	`reads_mapped`	read_count
\|\|	Samtools Stats	% Mapped	% Mapped Reads	`reads_mapped_percent`	None
\|\|	Samtools Stats	% Proper Pairs	% Properly Paired Reads	`reads_properly_paired_percent`	None
\|\|	Samtools Stats	% MapQ 0 Reads	% of Reads that are Ambiguously Placed (MapQ=0)	`reads_MQ0_percent`	None
\|\|	Samtools Stats	M Total seqs	Total sequences in the bam file (millions)	`raw_total_sequences`	read_count
\|\|	FastQC	% Dups	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC	% GC	Average % GC Content	`percent_gc`	None
\|\|	FastQC	Length	Average Sequence Length (bp)	`avg_sequence_length`	None
\|\|	FastQC	% Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	FastQC	M Seqs	Total Sequences (millions)	`total_sequences`	read_count

QualiMap

QualiMap is a platform-independent application to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.

Coverage histogram

Distribution of the number of locations in the reference genome with a given depth of coverage.

Bases of a reference sequence (y-axis) are groupped by their depth of coverage (0×, 1×, …, N×) (x-axis). This plot shows the frequency of coverage depths relative to the reference sequence for each read dataset, which provides an indirect measure of the level and variation of coverage depth in the corresponding sequenced sample.

If reads are randomly distributed across the reference sequence, this plot should resemble a Poisson distribution (Lander & Waterman 1988), with a peak indicating approximate depth of coverage, and more uniform coverage depth being reflected in a narrower spread. The optimal level of coverage depth depends on the aims of the experiment, though it should at minimum be sufficiently high to adequately address the biological question; greater uniformity of coverage is generally desirable, because it increases breadth of coverage for a given depth of coverage, allowing equivalent results to be achieved at a lower sequencing depth (Sampson et al. 2011; Sims et al. 2014). However, it is difficult to achieve uniform coverage depth in practice, due to biases introduced during sample preparation (van Dijk et al. 2014), sequencing (Ross et al. 2013) and read mapping (Sims et al. 2014).

This plot may include a small peak for regions of the reference sequence with zero depth of coverage. Such regions may be absent from the given sample (due to a deletion or structural rearrangement), present in the sample but not successfully sequenced (due to bias in sequencing or preparation), or sequenced but not successfully mapped to the reference (due to the choice of mapping algorithm, the presence of repeat sequences, or mismatches caused by variants or sequencing errors). Related factors cause most datasets to contain some unmapped reads (Sims et al. 2014).

Cumulative genome coverage

Percentage of the reference genome with at least the given depth of coverage.

For a set of DNA or RNA reads mapped to a reference sequence, such as a genome or transcriptome, the depth of coverage at a given base position is the number of high-quality reads that map to the reference at that position, while the breadth of coverage is the fraction of the reference sequence to which reads have been mapped with at least a given depth of coverage (Sims et al. 2014).

Defining coverage breadth in terms of coverage depth is useful, because sequencing experiments typically require a specific minimum depth of coverage over the region of interest (Sims et al. 2014), so the extent of the reference sequence that is amenable to analysis is constrained to lie within regions that have sufficient depth. With inadequate sequencing breadth, it can be difficult to distinguish the absence of a biological feature (such as a gene) from a lack of data (Green 2007).

For increasing coverage depths (1×, 2×, …, N×), coverage breadth is calculated as the percentage of the reference sequence that is covered by at least that number of reads, then plots coverage breadth (y-axis) against coverage depth (x-axis). This plot shows the relationship between sequencing depth and breadth for each read dataset, which can be used to gauge, for example, the likely effect of a minimum depth filter on the fraction of a genome available for analysis.

Insert size histogram

Distribution of estimated insert sizes of mapped reads.

To overcome limitations in the length of DNA or RNA sequencing reads, many sequencing instruments can produce two or more shorter reads from one longer fragment in which the relative position of reads is approximately known, such as paired-end or mate-pair reads (Mardis 2013). Such techniques can extend the reach of sequencing technology, allowing for more accurate placement of reads (Reinert et al. 2015) and better resolution of repeat regions (Reinert et al. 2015), as well as detection of structural variation (Alkan et al. 2011) and chimeric transcripts (Maher et al. 2009).

All these methods assume that the approximate size of an insert is known. (Insert size can be defined as the length in bases of a sequenced DNA or RNA fragment, excluding technical sequences such as adapters, which are typically removed before alignment.) This plot allows for that assumption to be assessed. With the set of mapped fragments for a given sample, QualiMap groups the fragments by insert size, then plots the frequency of mapped fragments (y-axis) over a range of insert sizes (x-axis). In an ideal case, the distribution of fragment sizes for a sequencing library would culminate in a single peak indicating average insert size, with a narrow spread indicating highly consistent fragment lengths.

QualiMap calculates insert sizes as follows: for each fragment in which every read mapped successfully to the same reference sequence, it extracts the insert size from the TLEN field of the leftmost read (see the Qualimap 2 documentation), where the TLEN (or 'observed Template LENgth') field contains 'the number of bases from the leftmost mapped base to the rightmost mapped base' (SAM format specification). Note that because it is defined in terms of alignment to a reference sequence, the value of the TLEN field may differ from the insert size due to factors such as alignment clipping, alignment errors, or structural variation or splicing in a gap between reads from the same fragment.

GC content distribution

Each solid line represents the distribution of GC content of mapped reads for a given sample. The dotted line represents a pre-calculated GC distribution for the reference genome.

GC bias is the difference between the guanine-cytosine content (GC-content) of a set of sequencing reads and the GC-content of the DNA or RNA in the original sample. It is a well-known issue with sequencing systems, and may be introduced by PCR amplification, among other factors (Benjamini & Speed 2012; Ross et al. 2013).

QualiMap calculates the GC-content of individual mapped reads, then groups those reads by their GC-content (1%, 2%, …, 100%), and plots the frequency of mapped reads (y-axis) at each level of GC-content (x-axis). This plot shows the GC-content distribution of mapped reads for each read dataset, which should ideally resemble that of the original sample. It can be useful to display the GC-content distribution of an appropriate reference sequence for comparison, and QualiMap has an option to do this (see the Qualimap 2 documentation).

Bcftools

Bcftools contains utilities for variant calling and manipulating VCFs and BCFs.

Variant Substitution Types

Variant Quality

Indel Distribution

Variant depths

Read depth support distribution for called variants

Samtools

Samtools is a suite of programs for interacting with high-throughput sequencing data.

Percent Mapped

Alignment metrics from samtools stats; mapped vs. unmapped reads.

For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

Alignment metrics

This module parses the output from samtools stats. All numbers in millions.

FastQC

FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

Sequence Counts

Sequence counts for each sample. Duplicate read counts are an estimate only.

This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

Sequence Quality Histograms

The mean quality value across each base position in the read.

To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

Taken from the FastQC help:

The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

Per Sequence Quality Scores

The number of reads with average quality scores. Shows if a subset of reads has poor quality.

From the FastQC help:

The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

Per Base Sequence Content

The proportion of each base position for which each of the four normal DNA bases has been called.

To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

To see the data as a line plot, as in the original FastQC graph, click on a sample track.

From the FastQC help:

Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

Click a sample row to see a line plot for that dataset.

Rollover for sample name

Position: -

%T: -

%C: -

%A: -

%G: -

Per Sequence GC Content

The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

From the FastQC help:

This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

Per Base N Content

The percentage of base calls at each position for which an N was called.

From the FastQC help:

If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

Sequence Length Distribution

The distribution of fragment sizes (read lengths) found. See the FastQC help

Sequence Duplication Levels

The relative level of duplication found for every sequence.

From the FastQC Help:

In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

Overrepresented sequences

The total amount of overrepresented sequences found in each library.

FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

From the FastQC Help:

A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

194 samples had less than 1% of reads made up of overrepresented sequences

Adapter Content

The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

Note that only samples with ≥ 0.1% adapter contamination are shown.

There may be several lines per sample, as one is shown for each adapter detected in the file.

From the FastQC Help:

The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

No samples found with any adapter contamination > 0.1%

Status Checks

Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

v1.8

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Coverage histogram

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Sequence Duplication Levels

Overrepresented sequences

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