MultiQC Report

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

JavaScript Disabled

MultiQC reports use JavaScript for plots and toolbox functions. It looks like you have JavaScript disabled in your web browser. Please note that many of the report functions will not work as intended.

Report generated on 2021-02-06, 12:37 based on data in: /data/putnamlab/sgurr/Geoduck_TagSeq/output/fastp_multiQC

General Statistics

Showing ²⁸³/₂₈₃ rows and ⁷/₁₁ columns.

Sample Name	% Duplication	M Q30 reads	Mb Q30 bases	GC content	% PF	% Adapter	% Dups	% GC	Length	% Failed	M Seqs
clean.SG100_S152_L001_R1_001							19.1%	39%	96 bp	18%	2.7
clean.SG100_S152_L002_R1_001							18.1%	39%	96 bp	18%	2.7
clean.SG101_S156_L001_R1_001							24.6%	41%	98 bp	9%	2.5
clean.SG101_S156_L002_R1_001							23.5%	41%	98 bp	9%	2.5
clean.SG102_S160_L001_R1_001							16.8%	39%	95 bp	18%	2.1
clean.SG102_S160_L002_R1_001							15.9%	39%	95 bp	18%	2.0
clean.SG103_S164_L001_R1_001							22.2%	40%	98 bp	18%	2.5
clean.SG103_S164_L002_R1_001							21.2%	40%	98 bp	18%	2.4
clean.SG104_S168_L001_R1_001							20.4%	40%	96 bp	18%	2.3
clean.SG104_S168_L002_R1_001							19.4%	40%	96 bp	18%	2.2
clean.SG105_S172_L001_R1_001							48.5%	40%	99 bp	9%	2.7
clean.SG105_S172_L002_R1_001							47.4%	40%	99 bp	9%	2.6
clean.SG106_S176_L001_R1_001							24.9%	40%	95 bp	18%	3.8
clean.SG106_S176_L002_R1_001							23.9%	40%	95 bp	18%	3.7
clean.SG107_S180_L001_R1_001							18.9%	39%	96 bp	18%	2.5
clean.SG107_S180_L002_R1_001							17.7%	39%	96 bp	18%	2.5
clean.SG108_S183_L001_R1_001							20.8%	40%	96 bp	18%	2.4
clean.SG108_S183_L002_R1_001							19.7%	40%	96 bp	18%	2.4
clean.SG109_S141_L001_R1_001							19.3%	39%	96 bp	18%	2.0
clean.SG109_S141_L002_R1_001							18.6%	39%	96 bp	18%	1.9
clean.SG10_S116_L001_R1_001							23.2%	41%	94 bp	18%	2.6
clean.SG10_S116_L002_R1_001							22.3%	41%	94 bp	18%	2.6
clean.SG110_S145_L001_R1_001							15.8%	39%	97 bp	9%	2.0
clean.SG110_S145_L002_R1_001							14.5%	39%	97 bp	9%	1.9
clean.SG111_S149_L001_R1_001							17.9%	39%	96 bp	18%	2.4
clean.SG111_S149_L002_R1_001							16.8%	39%	96 bp	18%	2.3
clean.SG112_S153_L001_R1_001							22.0%	39%	95 bp	18%	2.7
clean.SG112_S153_L002_R1_001							20.6%	39%	95 bp	18%	2.6
clean.SG113_S157_L001_R1_001							20.1%	40%	96 bp	18%	2.3
clean.SG113_S157_L002_R1_001							18.7%	40%	96 bp	18%	2.3
clean.SG114_S161_L001_R1_001							18.3%	39%	96 bp	9%	2.5
clean.SG114_S161_L002_R1_001							17.3%	39%	96 bp	9%	2.5
clean.SG115_S165_L001_R1_001							19.0%	40%	97 bp	9%	2.3
clean.SG115_S165_L002_R1_001							18.1%	40%	97 bp	9%	2.3
clean.SG116_S169_L001_R1_001							19.5%	39%	96 bp	18%	2.4
clean.SG116_S169_L002_R1_001							18.3%	39%	96 bp	18%	2.3
clean.SG117_S173_L001_R1_001							21.2%	39%	95 bp	18%	3.2
clean.SG117_S173_L002_R1_001							20.0%	39%	95 bp	18%	3.1
clean.SG118_S177_L001_R1_001							22.6%	40%	96 bp	18%	2.4
clean.SG118_S177_L002_R1_001							21.6%	40%	96 bp	18%	2.3
clean.SG119_S181_L001_R1_001							21.2%	39%	96 bp	18%	2.3
clean.SG119_S181_L002_R1_001							20.3%	39%	96 bp	18%	2.3
clean.SG11_S124_L001_R1_001							41.1%	44%	98 bp	18%	2.6
clean.SG11_S124_L002_R1_001							40.1%	44%	98 bp	18%	2.5
clean.SG120_S184_L001_R1_001							17.6%	39%	96 bp	18%	1.7
clean.SG120_S184_L002_R1_001							16.4%	39%	96 bp	18%	1.6
clean.SG121_S142_L001_R1_001							19.0%	39%	96 bp	18%	3.1
clean.SG121_S142_L002_R1_001							17.9%	39%	96 bp	18%	3.0
clean.SG122_S146_L001_R1_001							18.5%	40%	95 bp	18%	3.0
clean.SG122_S146_L002_R1_001							17.5%	40%	95 bp	18%	3.0
clean.SG123_S150_L001_R1_001							20.0%	40%	96 bp	9%	2.3
clean.SG123_S150_L002_R1_001							19.0%	40%	96 bp	9%	2.3
clean.SG124_S154_L001_R1_001							20.7%	39%	95 bp	18%	3.4
clean.SG124_S154_L002_R1_001							19.4%	39%	95 bp	18%	3.3
clean.SG125_S158_L001_R1_001							20.0%	39%	95 bp	18%	3.2
clean.SG125_S158_L002_R1_001							19.2%	39%	95 bp	18%	3.2
clean.SG126_S162_L001_R1_001							23.6%	40%	98 bp	9%	3.0
clean.SG126_S162_L002_R1_001							22.5%	40%	98 bp	9%	2.9
clean.SG127_S166_L001_R1_001							21.7%	40%	96 bp	18%	2.3
clean.SG127_S166_L002_R1_001							20.4%	40%	96 bp	18%	2.3
clean.SG128_S170_L001_R1_001							26.5%	41%	96 bp	18%	2.6
clean.SG128_S170_L002_R1_001							25.5%	41%	96 bp	18%	2.5
clean.SG129_S174_L001_R1_001							22.4%	40%	96 bp	18%	1.9
clean.SG129_S174_L002_R1_001							21.4%	40%	96 bp	18%	1.9
clean.SG12_S132_L001_R1_001							22.8%	41%	96 bp	18%	2.9
clean.SG12_S132_L002_R1_001							22.0%	41%	96 bp	18%	2.9
clean.SG130_S178_L001_R1_001							19.6%	39%	96 bp	18%	1.8
clean.SG130_S178_L002_R1_001							18.4%	39%	96 bp	18%	1.8
clean.SG131_S182_L001_R1_001							19.6%	40%	97 bp	18%	2.3
clean.SG131_S182_L002_R1_001							18.5%	40%	97 bp	18%	2.3
clean.SG132_S185_L001_R1_001							20.7%	39%	97 bp	9%	2.3
clean.SG132_S185_L002_R1_001							19.6%	39%	97 bp	18%	2.2
clean.SG133_S143_L001_R1_001							23.2%	39%	98 bp	9%	3.2
clean.SG133_S143_L002_R1_001							21.9%	39%	98 bp	9%	3.1
clean.SG134_S147_L001_R1_001							19.2%	39%	95 bp	18%	2.1
clean.SG134_S147_L002_R1_001							18.2%	39%	95 bp	18%	2.0
clean.SG135_S151_L001_R1_001							22.1%	40%	95 bp	18%	1.8
clean.SG135_S151_L002_R1_001							20.9%	40%	95 bp	18%	1.8
clean.SG136_S155_L001_R1_001							16.5%	39%	95 bp	18%	1.8
clean.SG136_S155_L002_R1_001							15.5%	39%	95 bp	18%	1.8
clean.SG137_S159_L001_R1_001							21.0%	40%	96 bp	18%	2.4
clean.SG137_S159_L002_R1_001							19.9%	40%	96 bp	18%	2.3
clean.SG138_S163_L001_R1_001							19.1%	40%	96 bp	18%	1.9
clean.SG138_S163_L002_R1_001							18.3%	40%	95 bp	18%	1.8
clean.SG139_S167_L001_R1_001							21.5%	39%	96 bp	18%	2.7
clean.SG139_S167_L002_R1_001							20.4%	39%	96 bp	18%	2.7
clean.SG13_S46_L001_R1_001							21.6%	41%	97 bp	9%	2.4
clean.SG13_S46_L002_R1_001							20.6%	41%	97 bp	9%	2.3
clean.SG140_S171_L001_R1_001							20.4%	39%	95 bp	18%	2.2
clean.SG140_S171_L002_R1_001							19.1%	39%	95 bp	18%	2.2
clean.SG141_S175_L001_R1_001							19.6%	39%	98 bp	9%	1.9
clean.SG141_S175_L002_R1_001							18.4%	39%	98 bp	9%	1.8
clean.SG142_S179_L001_R1_001							20.7%	41%	97 bp	18%	2.0
clean.SG142_S179_L002_R1_001							19.7%	41%	97 bp	9%	2.0
clean.SG14_S54_L001_R1_001							23.3%	40%	94 bp	18%	2.7
clean.SG14_S54_L002_R1_001							22.1%	40%	94 bp	18%	2.7
clean.SG15_S62_L001_R1_001							19.9%	39%	95 bp	18%	2.6
clean.SG15_S62_L002_R1_001							18.9%	39%	95 bp	18%	2.5
clean.SG16_S70_L001_R1_001							21.0%	40%	95 bp	18%	2.5
clean.SG16_S70_L002_R1_001							20.0%	40%	95 bp	18%	2.5
clean.SG17_S78_L001_R1_001							22.2%	40%	95 bp	18%	3.0
clean.SG17_S78_L002_R1_001							21.1%	40%	95 bp	18%	3.0
clean.SG18_S86_L001_R1_001							23.1%	41%	94 bp	18%	2.9
clean.SG18_S86_L002_R1_001							22.1%	41%	94 bp	18%	2.9
clean.SG19_S94_L001_R1_001							23.1%	41%	95 bp	18%	2.5
clean.SG19_S94_L002_R1_001							22.1%	41%	95 bp	18%	2.5
clean.SG1_S45_L001_R1_001							20.0%	40%	94 bp	9%	2.5
clean.SG1_S45_L002_R1_001							19.1%	40%	94 bp	9%	2.5
clean.SG20_S102_L001_R1_001							22.2%	40%	95 bp	18%	2.3
clean.SG20_S102_L002_R1_001							21.3%	41%	95 bp	18%	2.3
clean.SG21_S109_L001_R1_001							25.3%	42%	98 bp	18%	1.9
clean.SG21_S109_L002_R1_001							24.0%	42%	98 bp	18%	1.9
clean.SG22_S117_L001_R1_001							23.9%	41%	97 bp	18%	1.9
clean.SG22_S117_L002_R1_001							23.0%	41%	97 bp	18%	1.9
clean.SG23_S125_L001_R1_001							22.6%	40%	96 bp	18%	2.4
clean.SG23_S125_L002_R1_001							21.6%	40%	96 bp	18%	2.3
clean.SG24_S133_L001_R1_001							22.4%	40%	96 bp	18%	3.3
clean.SG24_S133_L002_R1_001							21.3%	40%	96 bp	18%	3.2
clean.SG25_S47_L001_R1_001							22.2%	40%	94 bp	18%	2.2
clean.SG25_S47_L002_R1_001							21.3%	40%	94 bp	18%	2.2
clean.SG26_S55_L001_R1_001							21.3%	40%	95 bp	18%	2.5
clean.SG26_S55_L002_R1_001							20.3%	40%	95 bp	18%	2.5
clean.SG27_S63_L001_R1_001							25.5%	41%	97 bp	18%	2.2
clean.SG27_S63_L002_R1_001							24.5%	41%	97 bp	18%	2.1
clean.SG28_S71_L001_R1_001							21.7%	40%	96 bp	18%	2.3
clean.SG28_S71_L002_R1_001							20.7%	40%	96 bp	18%	2.2
clean.SG29_S79_L001_R1_001							22.8%	41%	98 bp	9%	3.0
clean.SG29_S79_L002_R1_001							21.7%	41%	98 bp	9%	2.9
clean.SG2_S53_L001_R1_001							19.5%	40%	94 bp	18%	2.9
clean.SG2_S53_L002_R1_001							18.6%	40%	94 bp	18%	2.8
clean.SG30_S87_L001_R1_001							20.6%	41%	97 bp	9%	2.7
clean.SG30_S87_L002_R1_001							19.5%	41%	97 bp	9%	2.7
clean.SG31_S95_L001_R1_001							23.5%	41%	95 bp	18%	2.5
clean.SG31_S95_L002_R1_001							22.7%	41%	95 bp	18%	2.5
clean.SG32_S103_L001_R1_001							20.6%	40%	96 bp	18%	2.3
clean.SG32_S103_L002_R1_001							19.4%	40%	96 bp	18%	2.3
clean.SG33_S110_L001_R1_001							21.5%	41%	97 bp	9%	2.6
clean.SG33_S110_L002_R1_001							20.6%	41%	96 bp	9%	2.5
clean.SG34_S118_L001_R1_001							23.3%	41%	95 bp	18%	1.9
clean.SG34_S118_L002_R1_001							22.5%	41%	95 bp	18%	1.9
clean.SG35_S126_L001_R1_001							22.2%	41%	97 bp	18%	2.1
clean.SG35_S126_L002_R1_001							20.9%	41%	97 bp	18%	2.0
clean.SG36_S134_L001_R1_001							24.1%	40%	97 bp	18%	3.3
clean.SG36_S134_L002_R1_001							23.2%	40%	97 bp	18%	3.3
clean.SG37_S48_L001_R1_001							21.7%	40%	94 bp	18%	2.9
clean.SG37_S48_L002_R1_001							20.5%	40%	94 bp	18%	2.8
clean.SG38_S56_L001_R1_001							24.0%	40%	94 bp	18%	2.3
clean.SG38_S56_L002_R1_001							23.4%	40%	94 bp	18%	2.3
clean.SG39_S64_L001_R1_001							25.0%	41%	94 bp	18%	2.2
clean.SG39_S64_L002_R1_001							23.9%	41%	94 bp	18%	2.2
clean.SG3_S61_L001_R1_001							17.4%	40%	95 bp	9%	2.7
clean.SG3_S61_L002_R1_001							16.4%	40%	95 bp	9%	2.7
clean.SG40_S72_L001_R1_001							25.1%	40%	95 bp	18%	2.4
clean.SG40_S72_L002_R1_001							24.2%	40%	95 bp	18%	2.4
clean.SG41_S80_L001_R1_001							22.7%	40%	94 bp	18%	3.2
clean.SG41_S80_L002_R1_001							21.5%	40%	94 bp	18%	3.2
clean.SG42_S88_L001_R1_001							20.3%	40%	95 bp	18%	2.4
clean.SG42_S88_L002_R1_001							19.3%	40%	95 bp	18%	2.4
clean.SG43_S96_L001_R1_001							22.6%	40%	95 bp	18%	2.8
clean.SG43_S96_L002_R1_001							21.8%	40%	94 bp	18%	2.7
clean.SG44_S104_L001_R1_001							23.7%	40%	95 bp	18%	2.9
clean.SG44_S104_L002_R1_001							22.8%	40%	94 bp	18%	2.9
clean.SG45_S111_L001_R1_001							24.8%	41%	95 bp	18%	2.4
clean.SG45_S111_L002_R1_001							23.8%	41%	95 bp	18%	2.3
clean.SG46_S119_L001_R1_001							23.6%	40%	95 bp	18%	2.6
clean.SG46_S119_L002_R1_001							22.6%	40%	95 bp	18%	2.5
clean.SG47_S127_L001_R1_001							21.5%	40%	96 bp	9%	2.2
clean.SG47_S127_L002_R1_001							20.8%	40%	96 bp	9%	2.1
clean.SG48_S135_L001_R1_001							27.1%	41%	96 bp	18%	3.0
clean.SG48_S135_L002_R1_001							26.0%	41%	96 bp	18%	3.0
clean.SG49_S49_L001_R1_001							24.7%	40%	95 bp	18%	3.3
clean.SG49_S49_L002_R1_001							23.6%	40%	95 bp	18%	3.3
clean.SG4_S69_L001_R1_001							21.4%	40%	95 bp	18%	2.4
clean.SG4_S69_L002_R1_001							20.7%	40%	95 bp	18%	2.4
clean.SG50_S57_L001_R1_001							19.4%	40%	95 bp	18%	2.3
clean.SG50_S57_L002_R1_001							18.5%	40%	95 bp	18%	2.3
clean.SG51_S65_L001_R1_001							20.5%	42%	95 bp	9%	2.2
clean.SG51_S65_L002_R1_001							19.6%	42%	95 bp	9%	2.2
clean.SG52_S73_L001_R1_001							22.8%	40%	96 bp	18%	2.5
clean.SG52_S73_L002_R1_001							22.1%	40%	96 bp	18%	2.5
clean.SG53_S81_L001_R1_001							22.3%	40%	97 bp	9%	3.4
clean.SG53_S81_L002_R1_001							21.2%	40%	96 bp	9%	3.3
clean.SG54_S89_L001_R1_001							23.1%	41%	95 bp	9%	2.5
clean.SG54_S89_L002_R1_001							22.0%	41%	95 bp	9%	2.5
clean.SG55_S97_L001_R1_001							36.6%	41%	99 bp	18%	3.5
clean.SG55_S97_L002_R1_001							35.3%	41%	99 bp	18%	3.4
clean.SG56_S105_L001_R1_001							26.4%	41%	96 bp	18%	3.1
clean.SG56_S105_L002_R1_001							25.5%	41%	96 bp	18%	3.1
clean.SG57_S112_L001_R1_001							29.6%	41%	96 bp	18%	2.9
clean.SG57_S112_L002_R1_001							28.6%	41%	96 bp	18%	2.9
clean.SG58_S120_L001_R1_001							24.3%	41%	95 bp	18%	2.3
clean.SG58_S120_L002_R1_001							23.4%	41%	95 bp	18%	2.2
clean.SG59_S128_L001_R1_001							26.7%	42%	96 bp	18%	1.9
clean.SG59_S128_L002_R1_001							25.9%	43%	96 bp	18%	1.9
clean.SG5_S77_L001_R1_001							23.8%	41%	95 bp	18%	3.0
clean.SG5_S77_L002_R1_001							22.9%	41%	95 bp	18%	3.0
clean.SG60_S136_L001_R1_001							26.1%	41%	96 bp	18%	2.4
clean.SG60_S136_L002_R1_001							25.1%	41%	96 bp	18%	2.4
clean.SG61_S50_L001_R1_001							23.6%	40%	95 bp	18%	2.9
clean.SG61_S50_L002_R1_001							22.6%	40%	95 bp	18%	2.8
clean.SG62_S58_L001_R1_001							21.7%	40%	95 bp	18%	2.7
clean.SG62_S58_L002_R1_001							20.8%	40%	95 bp	18%	2.7
clean.SG63_S66_L001_R1_001							23.5%	40%	95 bp	18%	3.1
clean.SG63_S66_L002_R1_001							22.2%	40%	95 bp	18%	3.0
clean.SG64_S74_L001_R1_001							20.4%	40%	96 bp	9%	2.5
clean.SG64_S74_L002_R1_001							19.4%	40%	96 bp	9%	2.5
clean.SG65_S82_L001_R1_001							23.4%	40%	95 bp	18%	3.0
clean.SG65_S82_L002_R1_001							22.5%	40%	95 bp	18%	2.9
clean.SG66_S90_L001_R1_001							26.3%	40%	97 bp	9%	2.5
clean.SG66_S90_L002_R1_001							25.1%	40%	97 bp	9%	2.5
clean.SG67_S98_L001_R1_001							20.2%	41%	95 bp	9%	2.7
clean.SG67_S98_L002_R1_001							19.4%	41%	95 bp	9%	2.6
clean.SG68_S106_L001_R1_001							23.5%	40%	95 bp	18%	3.1
clean.SG68_S106_L002_R1_001							22.6%	40%	95 bp	18%	3.1
clean.SG69_S113_L001_R1_001							23.5%	40%	96 bp	9%	2.8
clean.SG69_S113_L002_R1_001							22.6%	40%	96 bp	9%	2.8
clean.SG6_S85_L001_R1_001							20.8%	41%	95 bp	18%	2.6
clean.SG6_S85_L002_R1_001							19.9%	41%	94 bp	18%	2.5
clean.SG70_S121_L001_R1_001							19.8%	40%	95 bp	18%	2.4
clean.SG70_S121_L002_R1_001							18.9%	40%	95 bp	18%	2.4
clean.SG71_S129_L001_R1_001							23.7%	41%	95 bp	18%	2.0
clean.SG71_S129_L002_R1_001							22.7%	41%	95 bp	18%	1.9
clean.SG72_S137_L001_R1_001							22.3%	40%	96 bp	18%	2.5
clean.SG72_S137_L002_R1_001							21.1%	40%	96 bp	18%	2.4
clean.SG73_S51_L001_R1_001							18.0%	40%	95 bp	9%	2.4
clean.SG73_S51_L002_R1_001							16.9%	40%	95 bp	9%	2.3
clean.SG74_S59_L001_R1_001							19.0%	40%	94 bp	9%	2.0
clean.SG74_S59_L002_R1_001							18.1%	40%	93 bp	9%	2.0
clean.SG75_S67_L001_R1_001							21.5%	40%	94 bp	18%	2.0
clean.SG75_S67_L002_R1_001							20.6%	40%	94 bp	18%	2.0
clean.SG76_S75_L001_R1_001							22.1%	40%	94 bp	18%	2.2
clean.SG76_S75_L002_R1_001							21.3%	40%	94 bp	18%	2.2
clean.SG77_S83_L001_R1_001							19.6%	40%	94 bp	18%	2.4
clean.SG77_S83_L002_R1_001							18.7%	40%	94 bp	18%	2.4
clean.SG78_S91_L001_R1_001							15.6%	39%	94 bp	18%	2.0
clean.SG78_S91_L002_R1_001							14.4%	39%	94 bp	18%	1.9
clean.SG79_S99_L001_R1_001							17.3%	40%	95 bp	18%	2.0
clean.SG79_S99_L002_R1_001							16.4%	40%	95 bp	18%	2.0
clean.SG7_S93_L001_R1_001							22.5%	41%	95 bp	9%	2.9
clean.SG7_S93_L002_R1_001							21.6%	41%	95 bp	9%	2.9
clean.SG80_S107_L001_R1_001							17.3%	39%	95 bp	18%	1.9
clean.SG80_S107_L002_R1_001							16.1%	39%	95 bp	18%	1.9
clean.SG81_S114_L001_R1_001							19.4%	40%	94 bp	18%	1.9
clean.SG81_S114_L002_R1_001							18.2%	40%	94 bp	18%	1.8
clean.SG82_S122_L001_R1_001							19.1%	39%	95 bp	9%	2.0
clean.SG82_S122_L002_R1_001							18.0%	39%	95 bp	18%	2.0
clean.SG83_S130_L001_R1_001							18.6%	40%	95 bp	9%	1.9
clean.SG83_S130_L002_R1_001							17.6%	40%	95 bp	9%	1.9
clean.SG84_S138_L001_R1_001							21.1%	40%	94 bp	18%	2.6
clean.SG84_S138_L002_R1_001							20.3%	40%	94 bp	18%	2.6
clean.SG85_S52_L001_R1_001							21.2%	40%	95 bp	18%	3.7
clean.SG85_S52_L002_R1_001							20.3%	40%	95 bp	18%	3.6
clean.SG86_S60_L001_R1_001							23.2%	40%	95 bp	18%	3.7
clean.SG86_S60_L002_R1_001							22.2%	40%	95 bp	18%	3.6
clean.SG87_S68_L001_R1_001							28.5%	41%	95 bp	18%	3.8
clean.SG87_S68_L002_R1_001							27.5%	41%	95 bp	18%	3.8
clean.SG88_S76_L001_R1_001							24.2%	40%	95 bp	18%	2.9
clean.SG88_S76_L002_R1_001							23.3%	40%	95 bp	18%	2.9
clean.SG89_S84_L001_R1_001							22.0%	41%	97 bp	18%	3.0
clean.SG89_S84_L002_R1_001							20.9%	41%	96 bp	18%	2.9
clean.SG8_S101_L001_R1_001							22.0%	40%	96 bp	18%	3.0
clean.SG8_S101_L002_R1_001							20.8%	40%	95 bp	18%	3.0
clean.SG90_S92_L001_R1_001							20.2%	40%	96 bp	18%	3.2
clean.SG90_S92_L002_R1_001							19.0%	40%	96 bp	18%	3.1
clean.SG91_S100_L001_R1_001							20.1%	40%	96 bp	18%	2.7
clean.SG91_S100_L002_R1_001							19.1%	40%	96 bp	18%	2.6
clean.SG93_S115_L001_R1_001							22.1%	40%	97 bp	9%	2.5
clean.SG93_S115_L002_R1_001							21.1%	40%	97 bp	18%	2.4
clean.SG94_S123_L001_R1_001							19.6%	40%	94 bp	18%	2.1
clean.SG94_S123_L002_R1_001							18.7%	40%	94 bp	18%	2.1
clean.SG95_S131_L001_R1_001							29.0%	41%	98 bp	18%	2.2
clean.SG95_S131_L002_R1_001							27.9%	41%	98 bp	18%	2.1
clean.SG96_S139_L001_R1_001							22.4%	40%	97 bp	9%	1.9
clean.SG96_S139_L002_R1_001							21.3%	40%	97 bp	18%	1.9
clean.SG97_S140_L001_R1_001							21.8%	39%	94 bp	18%	3.1
clean.SG97_S140_L002_R1_001							20.9%	39%	94 bp	18%	3.0
clean.SG98_S144_L001_R1_001							27.9%	40%	95 bp	18%	3.4
clean.SG98_S144_L002_R1_001							26.6%	40%	95 bp	18%	3.4
clean.SG99_S148_L001_R1_001							18.5%	39%	95 bp	18%	2.7
clean.SG99_S148_L002_R1_001							17.6%	39%	95 bp	18%	2.6
clean.SG9_S108_L001_R1_001							25.2%	41%	97 bp	18%	2.7
clean.SG9_S108_L002_R1_001							24.1%	41%	97 bp	18%	2.7
fastp	50.2%	0.0	249.4	41.9%	83.0%	5.5%

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

Sort	Group	Column	Description	ID	Scale
\|\|	fastp	% Duplication	Duplication rate in filtered reads	`pct_duplication`	None
\|\|	fastp	M Q30 reads	Reads > Q30 after filtering (millions)	`after_filtering_q30_rate`	read_count
\|\|	fastp	Mb Q30 bases	Bases > Q30 after filtering (millions)	`after_filtering_q30_bases`	base_count
\|\|	fastp	GC content	GC content after filtering	`after_filtering_gc_content`	None
\|\|	fastp	% PF	Percent reads passing filter	`pct_surviving`	None
\|\|	fastp	% Adapter	Percentage adapter-trimmed reads	`pct_adapter`	None
\|\|	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

fastp

fastp An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...)

Filtered Reads

Filtering statistics of sampled reads.

Duplication Rates

Duplication rates of sampled reads.

Sequence Quality

Average sequencing quality over each base of all reads.

GC Content

Average GC content over each base of all reads.

N content

Average N content over each base of all reads.

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.

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).

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.

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

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.

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.

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

v1.7

MultiQC Toolbox

Highlight Samples

Rename Samples

Show / Hide Samples

Export Plots

Choose Plots

Save Settings

Load Settings

About MultiQC

General Statistics

fastp

Filtered Reads

Duplication Rates

Sequence Quality

GC Content

N content

FastQC

Sequence Counts

Sequence Quality Histograms

Per Sequence Quality Scores

Per Base Sequence Content

Rollover for sample name

Per Sequence GC Content

Per Base N Content

Sequence Length Distribution

Sequence Duplication Levels

Overrepresented sequences

Adapter Content

Toggle navigation v1.7

MultiQC Toolbox

Apply Highlight Samples

Apply Rename Samples

Apply Show / Hide Samples

Export Plots

Choose Plots

Save Settings

Load Settings

About MultiQC

General Statistics

General Statistics: Columns

fastp

Filtered Reads

Duplication Rates

Sequence Quality

GC Content

N content

FastQC

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

Sequence Duplication Levels Help

Overrepresented sequences Help

Adapter Content Help

v1.7

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

Sequence Duplication Levels

Overrepresented sequences

Adapter Content