MultiQC Report

General Statistics

Showing ⁵⁹/₁₁₈ rows and ⁵/₂₀ columns.

Sample Name	% Dups	% GC	Length	% Failed	Seqs	# Reads	% BP Trimmed	% Dups	% GC	Length	% Failed	Seqs	# Reads	Aligned	% Aligned	% BS Conversion	Insert Size	Mean Insert Size	# Unique CpG	Avg. CpG Coverage
zr10604_10_R1	91.6%	34%	151 bp	36%	27424	27424	9.3%	91.6%	33%	137 bp	36%	27416	27416	24356	88.8%	99.8%	144 bp	145 bp	53	5724X
zr10604_10_R2	87.8%	35%	151 bp	64%	27424		9.3%	87.9%	33%	137 bp	64%	27416
zr10604_11_R1	92.2%	34%	151 bp	36%	23696	23696	9.2%	92.2%	32%	137 bp	36%	23693	23693	21713	91.6%	99.8%	144 bp	147 bp	53	5510X
zr10604_11_R2	88.7%	34%	151 bp	64%	23696		9.1%	88.7%	33%	137 bp	64%	23693
zr10604_12_R1	91.0%	35%	151 bp	36%	35223	35223	19.2%	91.1%	33%	121 bp	36%	35205	35205	27204	77.3%	99.7%	144 bp	141 bp	53	6229X
zr10604_12_R2	88.9%	36%	151 bp	64%	35223		19.1%	89.0%	34%	122 bp	64%	35205
zr10604_13_R1	92.0%	35%	151 bp	36%	37762	37762	17.4%	92.0%	33%	124 bp	36%	37733	37733	29355	77.8%	99.8%	144 bp	145 bp	53	7254X
zr10604_13_R2	87.0%	35%	151 bp	64%	37762		17.1%	87.1%	33%	125 bp	64%	37733
zr10604_14_R1	93.2%	35%	151 bp	36%	56527	56527	36.5%	93.4%	33%	96 bp	36%	56513	56513	30176	53.4%	99.8%	144 bp	137 bp	53	6382X
zr10604_14_R2	92.1%	37%	151 bp	64%	56527		36.4%	92.2%	34%	96 bp	64%	56513
zr10604_15_R1	93.2%	34%	151 bp	36%	31838	31838	8.9%	93.2%	32%	137 bp	36%	31831	31831	29559	92.9%	99.8%	144 bp	147 bp	53	7499X
zr10604_15_R2	90.6%	34%	151 bp	64%	31838		8.8%	90.6%	33%	137 bp	64%	31831
zr10604_16_R1	91.4%	34%	151 bp	36%	26002	26002	16.5%	91.3%	33%	126 bp	36%	25994	25994	20944	80.6%	99.8%	144 bp	142 bp	53	4903X
zr10604_16_R2	87.1%	35%	151 bp	64%	26002		16.3%	87.0%	33%	126 bp	64%	25994
zr10604_17_R1	92.5%	35%	151 bp	36%	53034	53034	21.3%	92.3%	33%	119 bp	36%	53015	53015	36746	69.3%	99.8%	144 bp	142 bp	53	7660X
zr10604_17_R2	88.8%	35%	151 bp	64%	53034		21.4%	88.6%	33%	119 bp	64%	53015
zr10604_18_R1	91.7%	35%	151 bp	36%	49007	49007	31.1%	91.7%	33%	104 bp	36%	48991	48991	29226	59.7%	99.9%	144 bp	140 bp	53	6680X
zr10604_18_R2	90.6%	36%	151 bp	64%	49007		31.0%	90.7%	33%	104 bp	64%	48991
zr10604_19_R1	92.1%	34%	151 bp	36%	32083	32083	10.8%	92.1%	33%	134 bp	36%	32075	32075	29576	92.2%	99.6%	144 bp	141 bp	53	6703X
zr10604_19_R2	90.3%	34%	151 bp	64%	32083		10.6%	90.3%	33%	135 bp	64%	32075
zr10604_1_R1	93.0%	36%	151 bp	36%	61943	61943	45.6%	93.2%	35%	82 bp	36%	61884	61884	23791	38.4%	99.3%	119 bp	127 bp	53	4176X
zr10604_1_R2	87.6%	39%	151 bp	64%	61943		44.6%	88.0%	35%	84 bp	64%	61884
zr10604_20_R1	91.8%	34%	151 bp	36%	29068	29068	12.0%	91.8%	32%	132 bp	36%	29065	29065	25791	88.7%	99.8%	144 bp	141 bp	53	5930X
zr10604_20_R2	90.1%	34%	151 bp	64%	29068		11.9%	90.1%	33%	133 bp	64%	29065
zr10604_21_R1	92.5%	36%	151 bp	36%	69657	69657	39.2%	92.6%	34%	92 bp	36%	69606	69606	30284	43.5%	99.7%	144 bp	144 bp	53	7260X
zr10604_21_R2	88.7%	38%	151 bp	64%	69657		38.5%	88.8%	35%	93 bp	64%	69606
zr10604_22_R1	91.8%	34%	151 bp	36%	37151	37151	12.2%	91.8%	33%	132 bp	36%	37136	37136	32321	87.0%	99.9%	144 bp	145 bp	53	7858X
zr10604_22_R2	89.0%	35%	151 bp	64%	37151		12.1%	89.0%	33%	133 bp	64%	37136
zr10604_23_R1	91.0%	35%	151 bp	36%	25161	25161	12.7%	90.9%	33%	131 bp	36%	25148	25148	20966	83.4%	99.7%	144 bp	143 bp	53	4736X
zr10604_23_R2	88.1%	35%	151 bp	64%	25161		12.6%	88.0%	33%	132 bp	64%	25148
zr10604_24_R1	90.1%	37%	151 bp	36%	59616	59616	38.0%	89.7%	35%	94 bp	36%	59608	59608	23169	38.9%	99.5%	144 bp	141 bp	53	5362X
zr10604_24_R2	87.8%	38%	151 bp	64%	59616		38.0%	87.5%	35%	94 bp	64%	59608
zr10604_25_R1	92.8%	34%	151 bp	36%	40351	40351	9.6%	92.8%	32%	136 bp	36%	40335	40335	36864	91.4%	99.6%	144 bp	145 bp	53	9117X
zr10604_25_R2	90.2%	34%	151 bp	64%	40351		9.5%	90.2%	33%	136 bp	64%	40335
zr10604_26_R1	92.5%	33%	151 bp	36%	37852	37852	10.0%	92.6%	32%	135 bp	36%	37841	37841	34614	91.5%	99.5%	144 bp	145 bp	53	8452X
zr10604_26_R2	90.2%	34%	151 bp	64%	37852		9.8%	90.2%	33%	136 bp	64%	37841
zr10604_27_R1	92.7%	34%	151 bp	36%	41759	41759	11.6%	92.7%	33%	133 bp	36%	41752	41752	36475	87.4%	99.9%	144 bp	146 bp	53	9139X
zr10604_27_R2	89.7%	34%	151 bp	64%	41759		11.5%	89.8%	33%	133 bp	64%	41752
zr10604_28_R1	92.5%	34%	151 bp	36%	45289	45289	9.5%	92.5%	32%	136 bp	36%	45267	45267	40809	90.2%	99.7%	144 bp	146 bp	53	10332X
zr10604_28_R2	88.4%	34%	151 bp	64%	45289		9.5%	88.5%	33%	137 bp	64%	45267
zr10604_29_R1	93.2%	34%	151 bp	36%	44076	44076	10.8%	93.2%	33%	134 bp	36%	44066	44066	38581	87.6%	99.6%	144 bp	147 bp	53	9815X
zr10604_29_R2	90.2%	34%	151 bp	64%	44076		10.7%	90.2%	33%	135 bp	64%	44066
zr10604_2_R1	92.0%	37%	151 bp	36%	51144	51144	51.1%	91.6%	35%	74 bp	36%	51094	51094	14313	28.0%	97.7%	116 bp	116 bp	52	2590X
zr10604_2_R2	90.4%	39%	151 bp	64%	51144		50.9%	90.2%	36%	74 bp	64%	51094
zr10604_30_R1	92.5%	35%	151 bp	36%	53976	53976	27.2%	92.5%	33%	110 bp	36%	53945	53945	34418	63.8%	99.6%	144 bp	146 bp	53	8658X
zr10604_30_R2	89.0%	36%	151 bp	64%	53976		26.9%	89.1%	33%	111 bp	64%	53945
zr10604_31_R1	91.9%	34%	151 bp	36%	32312	32312	11.2%	91.9%	33%	134 bp	36%	32302	32302	28657	88.7%	99.8%	144 bp	146 bp	53	7142X
zr10604_31_R2	89.4%	34%	151 bp	64%	32312		11.1%	89.5%	33%	134 bp	64%	32302
zr10604_32_R1	92.6%	35%	151 bp	36%	55307	55307	21.4%	92.7%	33%	118 bp	36%	55288	55288	41418	74.9%	99.8%	144 bp	142 bp	53	9797X
zr10604_32_R2	91.0%	35%	151 bp	64%	55307		21.2%	91.1%	33%	119 bp	64%	55288
zr10604_33_R1	90.7%	37%	151 bp	36%	53852	53852	10.2%	90.7%	36%	135 bp	36%	53825	53825	48003	89.2%	99.7%	144 bp	145 bp	53	11670X
zr10604_33_R2	88.1%	37%	151 bp	64%	53852		10.1%	88.1%	36%	135 bp	64%	53825
zr10604_34_R1	91.5%	34%	151 bp	36%	32885	32885	9.6%	91.5%	33%	136 bp	36%	32864	32864	29558	89.9%	99.5%	144 bp	146 bp	53	7319X
zr10604_34_R2	87.7%	34%	151 bp	64%	32885		9.5%	87.7%	33%	136 bp	64%	32864
zr10604_35_R1	91.9%	36%	151 bp	36%	45165	45165	9.4%	91.9%	35%	136 bp	36%	45146	45146	41454	91.8%	99.6%	144 bp	145 bp	53	10089X
zr10604_35_R2	88.5%	36%	151 bp	64%	45165		9.3%	88.6%	35%	137 bp	64%	45146
zr10604_36_R1	92.3%	34%	151 bp	36%	65265	65265	9.6%	92.3%	33%	136 bp	36%	65257	65257	56073	85.9%	99.7%	154 bp	147 bp	53	13954X
zr10604_36_R2	89.7%	34%	151 bp	64%	65265		9.5%	89.7%	33%	136 bp	64%	65257
zr10604_37_R1	92.4%	35%	151 bp	36%	96424	96424	23.3%	92.4%	34%	115 bp	36%	96353	96353	62027	64.4%	99.7%	144 bp	148 bp	53	15723X
zr10604_37_R2	86.9%	36%	151 bp	64%	96424		23.1%	86.8%	34%	116 bp	64%	96353
zr10604_38_R1	92.6%	35%	151 bp	36%	66098	66098	34.2%	92.7%	33%	99 bp	36%	66083	66083	35323	53.5%	99.5%	144 bp	143 bp	53	8627X
zr10604_38_R2	89.2%	37%	151 bp	64%	66098		33.8%	89.2%	34%	100 bp	64%	66083
zr10604_39_R1	91.6%	34%	151 bp	36%	28309	28309	10.1%	91.6%	33%	135 bp	36%	28306	28306	25388	89.7%	99.5%	144 bp	146 bp	53	6257X
zr10604_39_R2	87.8%	34%	151 bp	64%	28309		9.9%	87.8%	33%	136 bp	64%	28306
zr10604_3_R1	91.6%	36%	151 bp	45%	54411	54411	53.0%	91.4%	35%	71 bp	36%	54395	54395	12656	23.3%	99.0%	119 bp	123 bp	53	2867X
zr10604_3_R2	90.7%	39%	151 bp	64%	54411		52.9%	90.7%	36%	71 bp	64%	54395
zr10604_40_R1	92.6%	34%	151 bp	36%	36585	36585	9.6%	92.6%	32%	136 bp	36%	36579	36579	33378	91.2%	99.7%	144 bp	146 bp	53	8318X
zr10604_40_R2	89.3%	34%	151 bp	64%	36585		9.5%	89.3%	33%	136 bp	64%	36579
zr10604_41_R1	93.1%	34%	151 bp	36%	28836	28836	9.8%	93.1%	32%	136 bp	36%	28820	28820	25804	89.5%	99.8%	144 bp	144 bp	53	6326X
zr10604_41_R2	86.0%	34%	151 bp	64%	28836		9.7%	86.0%	33%	136 bp	64%	28820
zr10604_42_R1	91.7%	35%	151 bp	36%	20513	20513	15.5%	91.7%	33%	127 bp	36%	20506	20506	16798	81.9%	99.7%	144 bp	147 bp	53	4242X
zr10604_42_R2	87.6%	35%	151 bp	64%	20513		15.3%	87.6%	34%	128 bp	64%	20506
zr10604_43_R1	91.6%	36%	151 bp	36%	37939	37939	22.9%	91.7%	34%	116 bp	36%	37934	37934	26629	70.2%	99.3%	144 bp	145 bp	53	6518X
zr10604_43_R2	87.5%	36%	151 bp	64%	37939		22.6%	87.7%	34%	117 bp	64%	37934
zr10604_44_R1	91.2%	35%	151 bp	36%	36754	36754	19.3%	91.3%	33%	121 bp	36%	36740	36740	27474	74.8%	99.8%	144 bp	146 bp	53	6828X
zr10604_44_R2	88.0%	36%	151 bp	64%	36754		19.1%	88.1%	34%	122 bp	64%	36740
zr10604_45_R1	91.3%	34%	151 bp	36%	20486	20486	11.1%	91.4%	33%	134 bp	36%	20482	20482	17672	86.3%	99.8%	144 bp	144 bp	53	4051X
zr10604_45_R2	88.9%	35%	151 bp	64%	20486		11.0%	89.0%	33%	134 bp	64%	20482
zr10604_46_R1	93.9%	35%	151 bp	36%	97649	97649	37.7%	94.1%	34%	94 bp	36%	97624	97624	48276	49.5%	99.8%	144 bp	145 bp	53	11748X
zr10604_46_R2	91.3%	37%	151 bp	64%	97649		37.3%	91.5%	34%	95 bp	64%	97624
zr10604_47_R1	91.7%	34%	151 bp	36%	22799	22799	10.4%	91.7%	33%	135 bp	36%	22795	22795	20241	88.8%	99.7%	144 bp	145 bp	53	4916X
zr10604_47_R2	83.8%	35%	151 bp	64%	22799		10.2%	83.9%	34%	135 bp	64%	22795
zr10604_48_R1	91.0%	35%	151 bp	36%	26608	26608	17.5%	91.0%	33%	124 bp	36%	26597	26597	21040	79.1%	99.8%	144 bp	137 bp	53	3974X
zr10604_48_R2	89.3%	35%	151 bp	64%	26608		17.4%	89.2%	33%	125 bp	64%	26597
zr10604_49_R1	93.3%	36%	151 bp	36%	91321	91321	35.4%	93.4%	34%	98 bp	36%	91288	91288	49109	53.8%	99.9%	144 bp	139 bp	53	10986X
zr10604_49_R2	91.9%	37%	151 bp	64%	91321		35.2%	92.0%	34%	98 bp	64%	91288
zr10604_4_R1	90.2%	36%	151 bp	36%	73822	73822	38.6%	89.8%	34%	92 bp	36%	73794	73794	28080	38.1%	99.7%	144 bp	140 bp	53	6337X
zr10604_4_R2	89.1%	37%	151 bp	64%	73822		39.2%	88.8%	34%	92 bp	55%	73794
zr10604_50_R1	92.8%	37%	151 bp	36%	99591	99591	38.0%	93.0%	36%	94 bp	36%	99526	99526	60094	60.4%	99.8%	144 bp	124 bp	53	11574X
zr10604_50_R2	83.2%	39%	151 bp	64%	99591		36.1%	86.0%	37%	97 bp	64%	99526
zr10604_51_R1	91.9%	35%	151 bp	36%	46771	46771	24.2%	92.0%	34%	114 bp	36%	46758	46758	31357	67.1%	99.9%	144 bp	141 bp	53	6278X
zr10604_51_R2	90.0%	36%	151 bp	64%	46771		24.2%	90.0%	34%	114 bp	64%	46758
zr10604_52_R1	91.8%	36%	151 bp	36%	44405	44405	14.2%	91.6%	34%	129 bp	36%	44378	44378	36948	83.3%	99.9%	144 bp	143 bp	53	8634X
zr10604_52_R2	88.9%	36%	151 bp	64%	44405		14.0%	88.8%	34%	130 bp	64%	44378
zr10604_53_R1	92.6%	36%	151 bp	36%	92925	92925	36.0%	92.3%	35%	96 bp	36%	92866	92866	41181	44.3%	99.8%	144 bp	145 bp	53	10235X
zr10604_53_R2	89.9%	38%	151 bp	64%	92925		35.8%	89.8%	35%	97 bp	64%	92866
zr10604_54_R1	91.2%	36%	151 bp	36%	38281	38281	17.9%	90.9%	35%	124 bp	36%	38262	38262	27951	73.1%	99.9%	144 bp	143 bp	53	5712X
zr10604_54_R2	87.8%	37%	151 bp	64%	38281		17.6%	87.6%	36%	124 bp	64%	38262
zr10604_55_R1	92.0%	35%	151 bp	36%	31546	31546	12.8%	92.0%	33%	132 bp	36%	31543	31543	25737	81.6%	99.8%	144 bp	142 bp	53	6071X
zr10604_55_R2	89.2%	34%	151 bp	64%	31546		12.9%	89.2%	33%	131 bp	64%	31543
zr10604_56_R1	90.6%	37%	151 bp	36%	34231	34231	14.1%	90.4%	35%	130 bp	36%	34208	34208	27920	81.6%	99.8%	144 bp	140 bp	53	6214X
zr10604_56_R2	87.6%	37%	151 bp	64%	34231		14.1%	87.5%	36%	130 bp	64%	34208
zr10604_57_R1	91.8%	37%	151 bp	36%	65015	65015	25.9%	91.2%	35%	111 bp	36%	64989	64989	37655	57.9%	99.9%	144 bp	141 bp	53	7867X
zr10604_57_R2	88.6%	37%	151 bp	64%	65015		25.6%	88.2%	36%	112 bp	64%	64989
zr10604_58_R1	92.8%	34%	151 bp	36%	35053	35053	14.7%	92.8%	32%	128 bp	36%	35052	35052	29749	84.9%	99.8%	144 bp	146 bp	53	7605X
zr10604_58_R2	91.1%	35%	151 bp	64%	35053		14.6%	91.1%	33%	129 bp	64%	35052
zr10604_59_R1	90.1%	42%	151 bp	36%	16836	16836	9.6%	90.1%	41%	136 bp	36%	16826	16826	15214	90.4%	99.6%	144 bp	146 bp	53	3789X
zr10604_59_R2	86.0%	42%	151 bp	64%	16836		9.6%	86.0%	42%	136 bp	64%	16826
zr10604_5_R1	89.7%	35%	151 bp	36%	38784	38784	22.8%	88.4%	34%	116 bp	36%	38773	38773	21965	56.7%	99.8%	154 bp	158 bp	53	5943X
zr10604_5_R2	87.1%	36%	151 bp	64%	38784		22.8%	86.3%	35%	116 bp	64%	38773
zr10604_6_R1	91.5%	34%	151 bp	36%	26251	26251	13.4%	91.4%	33%	130 bp	36%	26249	26249	22395	85.3%	99.9%	144 bp	146 bp	53	5527X
zr10604_6_R2	89.6%	35%	151 bp	64%	26251		13.3%	89.5%	33%	131 bp	64%	26249
zr10604_7_R1	89.8%	34%	151 bp	36%	39099	39099	13.5%	89.8%	33%	130 bp	36%	39090	39090	32197	82.4%	99.8%	144 bp	145 bp	53	7798X
zr10604_7_R2	89.1%	35%	151 bp	64%	39099		14.6%	89.1%	33%	129 bp	64%	39090
zr10604_8_R1	91.1%	36%	151 bp	36%	65582	65582	38.6%	91.1%	34%	91 bp	36%	65560	65560	27290	41.6%	99.8%	144 bp	147 bp	53	6796X
zr10604_8_R2	90.2%	37%	151 bp	64%	65582		38.9%	90.3%	34%	91 bp	64%	65560
zr10604_9_R1	91.4%	35%	151 bp	36%	49807	49807	21.5%	91.5%	34%	118 bp	36%	49792	49792	35408	71.1%	99.7%	144 bp	145 bp	53	8451X
zr10604_9_R2	89.5%	36%	151 bp	64%	49807		21.4%	89.5%	34%	119 bp	64%	49792

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

Sort	Group	Column	Description	ID	Scale
\|\|	FastQC (raw)	% Dups	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC (raw)	% GC	Average % GC Content	`percent_gc`	None
\|\|	FastQC (raw)	Length	Average Sequence Length (bp)	`avg_sequence_length`	None
\|\|	FastQC (raw)	% Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	FastQC (raw)	Seqs	Total Sequences (ones)	`total_sequences`	read_count
\|\|	FastQC (raw)	# Reads	Total Reads (ones)	`sequences_in_total`	read_count
\|\|	Cutadapt	% BP Trimmed	% Total Base Pairs trimmed	`percent_trimmed`	None
\|\|	FastQC (trimmed)	% Dups	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC (trimmed)	% GC	Average % GC Content	`percent_gc`	None
\|\|	FastQC (trimmed)	Length	Average Sequence Length (bp)	`avg_sequence_length`	None
\|\|	FastQC (trimmed)	% Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	FastQC (trimmed)	Seqs	Total Sequences (ones)	`total_sequences`	read_count
\|\|	FastQC (trimmed)	# Reads	Total Reads (ones)	`sequences_in_total`	read_count
\|\|	Bismark	Aligned	Total Aligned Sequences (ones)	`aligned_reads`	read_count
\|\|	Bismark	% Aligned	Percent Aligned Uniquely Sequences	`percent_aligned`	None
\|\|	Bismark	% BS Conversion	Percent Bisulfite Conversion Rate	`percent_bs_conversion`	None
\|\|	Picard	Insert Size	Median Insert Size, all read orientations (bp)	`summed_median`	None
\|\|	Picard	Mean Insert Size	Mean Insert Size, all read orientations (bp)	`summed_mean`	None
\|\|	MethylDackel	# Unique CpG	Total Number of Unique CpG	`unique_cpg`	None
\|\|	MethylDackel	Avg. CpG Coverage	Average CpG Coverage	`average_cpg_coverage`	None

FastQC (raw)

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

This section of the report shows FastQC results before adapter and quality trimming.

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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%

Cutadapt

Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

Trimmed Sequence Lengths (3')

This plot shows the number of reads with certain lengths of adapter trimmed for the 3' end.

Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.

See the cutadapt documentation for more information on how these numbers are generated.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Filtered Reads

This plot shows the number of reads (single-end) or read pairs (paired-end) passing filters.

loading..

FastQC (trimmed)

This section of the report shows FastQC results after adapter and quality trimming.

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Sequence Length Distribution

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

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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%

Bismark

Bismark is a tool to map bisulfite converted sequence reads and determine cytosine methylation states.

Alignment Rates

loading..

Strand Alignment

All samples were run with --directional mode; alignments to complementary strands (CTOT, CTOB) were ignored.

loading..

Picard

Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

Insert Size

Plot shows the number of reads at a given insert size. Reads with different orientations are summed.

loading..

CpG Coverage

CpG Coverage shows the distribution of the detected CpG coverage in each library.

loading..

Download

This section contains links to download files, data and/or images generated by various bioinformatics tools. To download individual files, click on the corresponding links. The links will expire in 90 days.

Showing ⁵⁹/₅₉ rows and ⁵/₅ columns.

Sample Name	Trimmed Fastq R1	Trimmed Fastq R2	Alignment	Methylation Calling	Browser Track
zr10604_1	Download	Download	Download	Download	Download
zr10604_10	Download	Download	Download	Download	Download
zr10604_11	Download	Download	Download	Download	Download
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zr10604_6	Download	Download	Download	Download	Download
zr10604_7	Download	Download	Download	Download	Download
zr10604_8	Download	Download	Download	Download	Download
zr10604_9	Download	Download	Download	Download	Download

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

Sort	Column	Description	ID	Scale
\|\|	Trimmed Fastq R1	Trimmed fastq for reads in single-end or R1 in paired-end.	`tr1`	None
\|\|	Trimmed Fastq R2	Trimmed fastq for R2 in paired-end.	`tr2`	None
\|\|	Alignment	Aligned sequence reads of individual samples in bam format.	`bam`	None
\|\|	Methylation Calling	Methylation calling results in bedGraph format.	`bedgraph`	None
\|\|	Browser Track	Genome tracks for individual samples that includes methylation ratio and coverage in BigBed format.	`bigbed`	None

Project files

all_count_sheet.xlsx

Batch download instructions

Click here to get the script for batch download.

Open Terminal (Mac/Linux) or Windows Powershell (Windows).

Change directory to where the script is e.g. Downloads/.

Run bash download.ps1 (Mac/Linux).

Or run PowerShell -ExecutionPolicy Bypass -File .\download.ps1 (Windows).

Software

fastqc: 0.11.9
trimgalore: 0.6.6
bismark: 0.23.0
methyldackel: 0.5.2

Summary

Reference: https://hgdownload.cse.ucsc.edu/goldenpath/hg19/bigZips/hg19.fa.gz
Amplicons: download
R1 Trim 5': 0 bp
R1 Trim 3': 0 bp
R2 Trim 5': 0 bp
R2 Trim 3': 0 bp
Directionality: directional
Deduplication: false

Toggle navigation v1.11

MultiQC Toolbox

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About MultiQC

General Statistics

General Statistics: Columns

FastQC (raw)

Sequence Counts Help

Sequence Quality Histograms Help

Per Sequence Quality Scores Help

Per Base Sequence Content Help

Rollover for sample name

Per Sequence GC Content Help

Per Base N Content Help

Adapter Content Help

Cutadapt

Trimmed Sequence Lengths (3') Help

Filtered Reads

FastQC (trimmed)

Sequence Counts Help

Sequence Quality Histograms Help

Per Sequence Quality Scores Help

Per Base Sequence Content Help

Rollover for sample name

Per Sequence GC Content Help

Per Base N Content Help

Sequence Length Distribution

Adapter Content Help

Bismark

Alignment Rates

Strand Alignment

Picard

Insert Size

CpG Coverage

Download

Table Fgzk: Columns

Project files

Batch download instructions

Software

Summary

v1.11

Highlight Samples

Rename Samples

Show / Hide Samples

Sequence Counts

Sequence Quality Histograms

Per Sequence Quality Scores

Per Base Sequence Content

Per Sequence GC Content

Per Base N Content

Adapter Content

Trimmed Sequence Lengths (3')

Sequence Counts

Sequence Quality Histograms

Per Sequence Quality Scores

Per Base Sequence Content

Per Sequence GC Content

Per Base N Content

Adapter Content