MultiQC Report

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

General Statistics

Showing ⁹⁴/₉₄ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
000000000-CHT9C_l01_n01_10_d5_NW_RC1_F2_CA_7_09_6386_1	90.2%	43%	151	25%	0.5
000000000-CHT9C_l01_n01_10_d5_NW_RC1_F2_CA_7_09_6386_2	88.2%	44%	151	17%	0.3
000000000-CHT9C_l01_n01_11_dA1_NW_RC1_F2_CA_7_09_6390_1	89.2%	44%	151	17%	0.4
000000000-CHT9C_l01_n01_11_dA1_NW_RC1_F2_CA_7_09_6390_2	87.9%	44%	151	17%	0.3
000000000-CHT9C_l01_n01_12_dA3_NW_RC2_F3_CA_7_09_6363_1	89.4%	44%	151	17%	0.3
000000000-CHT9C_l01_n01_12_dA3_NW_RC2_F3_CA_7_09_6363_2	89.0%	44%	151	17%	0.3
000000000-CHT9C_l01_n01_13_dA3_NW_RC2_F3_CA_7_09_6366_1	90.2%	44%	151	25%	0.4
000000000-CHT9C_l01_n01_13_dA3_NW_RC2_F3_CA_7_09_6366_2	88.3%	44%	151	17%	0.3
000000000-CHT9C_l01_n01_14_dA3_NW_RC2_F3_CA_7_09_6384_1	88.0%	44%	151	25%	0.4
000000000-CHT9C_l01_n01_14_dA3_NW_RC2_F3_CA_7_09_6384_2	87.2%	45%	151	33%	0.4
000000000-CHT9C_l01_n01_15_dA3_NW_RC2_F3_CA_7_09_6388_1	89.6%	43%	151	33%	0.4
000000000-CHT9C_l01_n01_15_dA3_NW_RC2_F3_CA_7_09_6388_2	87.1%	44%	151	33%	0.3
000000000-CHT9C_l01_n01_16_dA3_NW_RC2_F3_CA_7_09_6391_1	89.0%	44%	151	25%	0.4
000000000-CHT9C_l01_n01_16_dA3_NW_RC2_F3_CA_7_09_6391_2	88.0%	44%	151	33%	0.3
000000000-CHT9C_l01_n01_1_d2_NW_DI_F1_CA_7_09_5456_1	89.7%	43%	151	25%	0.5
000000000-CHT9C_l01_n01_1_d2_NW_DI_F1_CA_7_09_5456_2	87.6%	44%	151	17%	0.3
000000000-CHT9C_l01_n01_2_d2_NW_DI_F1_CA_7_09_6361_1	88.9%	43%	151	25%	0.5
000000000-CHT9C_l01_n01_2_d2_NW_DI_F1_CA_7_09_6361_2	88.1%	44%	151	25%	0.4
000000000-CHT9C_l01_n01_3_d2_NW_DI_F1_CA_7_09_6364_1	90.0%	44%	151	33%	0.5
000000000-CHT9C_l01_n01_3_d2_NW_DI_F1_CA_7_09_6364_2	86.4%	44%	151	33%	0.3
000000000-CHT9C_l01_n01_4_d2_NW_D1_F1_CA_7_09_6382_1	89.1%	44%	151	17%	0.4
000000000-CHT9C_l01_n01_4_d2_NW_D1_F1_CA_7_09_6382_2	88.9%	44%	151	25%	0.4
000000000-CHT9C_l01_n01_5_2016_TS_FT_02_d2_NW_DI_F1_CA_7_09_6385_1	89.5%	44%	151	17%	0.4
000000000-CHT9C_l01_n01_5_2016_TS_FT_02_d2_NW_DI_F1_CA_7_09_6385_2	77.2%	44%	151	33%	0.1
000000000-CHT9C_l01_n01_6_d2_NW_DI_F1_CA_7_09_6389_1	87.9%	44%	151	33%	0.3
000000000-CHT9C_l01_n01_6_d2_NW_DI_F1_CA_7_09_6389_2	89.1%	44%	151	17%	0.4
000000000-CHT9C_l01_n01_7_dA1_NW_RC1_F2_CA_7_09_6362_1	87.4%	43%	151	25%	0.3
000000000-CHT9C_l01_n01_7_dA1_NW_RC1_F2_CA_7_09_6362_2	88.7%	44%	151	25%	0.4
000000000-CHT9C_l01_n01_8_dA1_NW_RC1_F2_CA_7_09_6365_1	88.9%	44%	151	25%	0.5
000000000-CHT9C_l01_n01_8_dA1_NW_RC1_F2_CA_7_09_6365_2	85.0%	45%	151	17%	0.3
000000000-CHT9C_l01_n01_9_d5_NW_RC1_F2_CA_7_09_6383_1	90.0%	43%	151	25%	0.4
000000000-CHT9C_l01_n01_9_d5_NW_RC1_F2_CA_7_09_6383_2	89.8%	44%	151	17%	0.4
000000000-CHT9C_l01_n01_A_Harbor_Seal_New_Hampshire_179629_2012_H3N8_1	90.4%	45%	151	25%	0.5
000000000-CHT9C_l01_n01_A_Harbor_Seal_New_Hampshire_179629_2012_H3N8_2	89.9%	43%	151	33%	0.4
000000000-CHT9C_l01_n01_A_Texas_50_2012_1	90.0%	44%	151	33%	0.4
000000000-CHT9C_l01_n01_A_Texas_50_2012_2	89.8%	43%	151	33%	0.4
000000000-CHT9C_l01_n01_BLANK_1	56.8%	48%	151	33%	0.0
000000000-CHT9C_l01_n01_BLANK_2	1.8%	45%	151	33%	0.0
000000000-CHT9C_l01_n01_NEGATIVE_1	56.5%	42%	151	33%	0.0
000000000-CHT9C_l01_n01_NEGATIVE_2	3.0%	46%	151	42%	0.0
000000000-CHT9C_l01_n01_PD7_PB2_04_1	95.4%	44%	151	17%	0.4
000000000-CHT9C_l01_n01_PD7_PB2_04_2	95.9%	43%	151	17%	0.4
000000000-CHT9C_l01_n01_PD7_PB2_4_1	95.9%	43%	151	17%	0.4
000000000-CHT9C_l01_n01_PD7_PB2_4_2	94.5%	43%	151	17%	0.3
000000000-CHT9C_l01_n01_pH1N1_p002_1	89.5%	45%	151	33%	0.4
000000000-CHT9C_l01_n01_pH1N1_p002_2	88.6%	44%	151	25%	0.4
000000000-CHT9C_l01_n01_undetermined	88.6%	48%	151	33%	1.0
000000000-CHT9C_l01_n02_10_d5_NW_RC1_F2_CA_7_09_6386_1	87.9%	43%	151	17%	0.5
000000000-CHT9C_l01_n02_10_d5_NW_RC1_F2_CA_7_09_6386_2	86.6%	44%	151	17%	0.3
000000000-CHT9C_l01_n02_11_dA1_NW_RC1_F2_CA_7_09_6390_1	85.9%	44%	151	17%	0.4
000000000-CHT9C_l01_n02_11_dA1_NW_RC1_F2_CA_7_09_6390_2	84.7%	44%	151	17%	0.3
000000000-CHT9C_l01_n02_12_dA3_NW_RC2_F3_CA_7_09_6363_1	86.5%	44%	151	17%	0.3
000000000-CHT9C_l01_n02_12_dA3_NW_RC2_F3_CA_7_09_6363_2	86.6%	44%	151	17%	0.3
000000000-CHT9C_l01_n02_13_dA3_NW_RC2_F3_CA_7_09_6366_1	86.3%	44%	151	17%	0.4
000000000-CHT9C_l01_n02_13_dA3_NW_RC2_F3_CA_7_09_6366_2	82.9%	44%	151	17%	0.3
000000000-CHT9C_l01_n02_14_dA3_NW_RC2_F3_CA_7_09_6384_1	86.6%	44%	151	17%	0.4
000000000-CHT9C_l01_n02_14_dA3_NW_RC2_F3_CA_7_09_6384_2	86.1%	45%	151	17%	0.4
000000000-CHT9C_l01_n02_15_dA3_NW_RC2_F3_CA_7_09_6388_1	86.8%	43%	151	17%	0.4
000000000-CHT9C_l01_n02_15_dA3_NW_RC2_F3_CA_7_09_6388_2	85.4%	44%	151	17%	0.3
000000000-CHT9C_l01_n02_16_dA3_NW_RC2_F3_CA_7_09_6391_1	84.3%	44%	151	25%	0.4
000000000-CHT9C_l01_n02_16_dA3_NW_RC2_F3_CA_7_09_6391_2	84.3%	44%	151	17%	0.3
000000000-CHT9C_l01_n02_1_d2_NW_DI_F1_CA_7_09_5456_1	87.5%	43%	151	17%	0.5
000000000-CHT9C_l01_n02_1_d2_NW_DI_F1_CA_7_09_5456_2	85.3%	44%	151	17%	0.3
000000000-CHT9C_l01_n02_2_d2_NW_DI_F1_CA_7_09_6361_1	87.0%	43%	151	17%	0.5
000000000-CHT9C_l01_n02_2_d2_NW_DI_F1_CA_7_09_6361_2	86.5%	44%	151	17%	0.4
000000000-CHT9C_l01_n02_3_d2_NW_DI_F1_CA_7_09_6364_1	87.2%	44%	151	17%	0.5
000000000-CHT9C_l01_n02_3_d2_NW_DI_F1_CA_7_09_6364_2	82.2%	44%	151	17%	0.3
000000000-CHT9C_l01_n02_4_d2_NW_D1_F1_CA_7_09_6382_1	86.6%	44%	151	17%	0.4
000000000-CHT9C_l01_n02_4_d2_NW_D1_F1_CA_7_09_6382_2	87.1%	44%	151	17%	0.4
000000000-CHT9C_l01_n02_5_2016_TS_FT_02_d2_NW_DI_F1_CA_7_09_6385_1	86.9%	44%	151	17%	0.4
000000000-CHT9C_l01_n02_5_2016_TS_FT_02_d2_NW_DI_F1_CA_7_09_6385_2	58.7%	44%	151	25%	0.1
000000000-CHT9C_l01_n02_6_d2_NW_DI_F1_CA_7_09_6389_1	87.0%	44%	151	25%	0.3
000000000-CHT9C_l01_n02_6_d2_NW_DI_F1_CA_7_09_6389_2	88.2%	44%	151	17%	0.4
000000000-CHT9C_l01_n02_7_dA1_NW_RC1_F2_CA_7_09_6362_1	85.1%	43%	151	17%	0.3
000000000-CHT9C_l01_n02_7_dA1_NW_RC1_F2_CA_7_09_6362_2	87.2%	44%	151	17%	0.4
000000000-CHT9C_l01_n02_8_dA1_NW_RC1_F2_CA_7_09_6365_1	86.1%	44%	151	17%	0.5
000000000-CHT9C_l01_n02_8_dA1_NW_RC1_F2_CA_7_09_6365_2	83.2%	45%	151	17%	0.3
000000000-CHT9C_l01_n02_9_d5_NW_RC1_F2_CA_7_09_6383_1	87.4%	43%	151	33%	0.4
000000000-CHT9C_l01_n02_9_d5_NW_RC1_F2_CA_7_09_6383_2	87.6%	44%	151	17%	0.4
000000000-CHT9C_l01_n02_A_Harbor_Seal_New_Hampshire_179629_2012_H3N8_1	86.2%	45%	151	25%	0.5
000000000-CHT9C_l01_n02_A_Harbor_Seal_New_Hampshire_179629_2012_H3N8_2	88.0%	43%	151	33%	0.4
000000000-CHT9C_l01_n02_A_Texas_50_2012_1	84.9%	44%	151	33%	0.4
000000000-CHT9C_l01_n02_A_Texas_50_2012_2	87.5%	43%	151	25%	0.4
000000000-CHT9C_l01_n02_BLANK_1	50.5%	49%	151	42%	0.0
000000000-CHT9C_l01_n02_BLANK_2	0.6%	44%	151	33%	0.0
000000000-CHT9C_l01_n02_NEGATIVE_1	51.9%	42%	151	33%	0.0
000000000-CHT9C_l01_n02_NEGATIVE_2	0.6%	44%	151	42%	0.0
000000000-CHT9C_l01_n02_PD7_PB2_04_1	90.3%	44%	151	17%	0.4
000000000-CHT9C_l01_n02_PD7_PB2_04_2	94.6%	43%	151	17%	0.4
000000000-CHT9C_l01_n02_PD7_PB2_4_1	91.8%	43%	151	17%	0.4
000000000-CHT9C_l01_n02_PD7_PB2_4_2	94.1%	43%	151	17%	0.3
000000000-CHT9C_l01_n02_pH1N1_p002_1	84.8%	45%	151	25%	0.4
000000000-CHT9C_l01_n02_pH1N1_p002_2	86.8%	44%	151	25%	0.4
000000000-CHT9C_l01_n02_undetermined	79.2%	45%	151	8%	1.0

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

Sort	Group	Column	Description	ID	Scale
\|\|	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

Lane 1 Demultiplexing Report

Lane 1 Demultiplexing Report
Total Read Count: Total number of PF (Passing Filter) reads in this library.
Portion: The proportion of reads that represent the individual library in the entire Library Pool

Showing ⁴⁷/₄₇ rows and ²/₂ columns.

Sample Name	Total Read Count	Portion (%)
undetermined_library	967,833	5.8
1_d2_NW_DI_F1_CA_7_09_5456_1	478,398	2.9
2_d2_NW_DI_F1_CA_7_09_6361_1	453,972	2.7
3_d2_NW_DI_F1_CA_7_09_6364_1	451,917	2.7
4_d2_NW_D1_F1_CA_7_09_6382_1	390,467	2.3
5_2016_TS_FT_02_d2_NW_DI_F1_CA_7_09_6385_1	372,189	2.2
6_d2_NW_DI_F1_CA_7_09_6389_1	318,354	1.9
7_dA1_NW_RC1_F2_CA_7_09_6362_1	296,691	1.8
8_dA1_NW_RC1_F2_CA_7_09_6365_1	462,269	2.8
9_d5_NW_RC1_F2_CA_7_09_6383_1	429,350	2.6
10_d5_NW_RC1_F2_CA_7_09_6386_1	456,047	2.7
11_dA1_NW_RC1_F2_CA_7_09_6390_1	393,785	2.4
12_dA3_NW_RC2_F3_CA_7_09_6363_1	340,876	2.0
13_dA3_NW_RC2_F3_CA_7_09_6366_1	401,936	2.4
14_dA3_NW_RC2_F3_CA_7_09_6384_1	422,950	2.5
15_dA3_NW_RC2_F3_CA_7_09_6388_1	439,482	2.6
16_dA3_NW_RC2_F3_CA_7_09_6391_1	371,025	2.2
A_Harbor_Seal_New_Hampshire_179629_2012_H3N8_1	455,692	2.7
pH1N1_p002_1	434,720	2.6
A_Texas_50_2012_1	446,538	2.7
BLANK_1	3,214	0.0
NEGATIVE_1	6,790	0.0
PD7_PB2_4_1	419,153	2.5
PD7_PB2_04_1	383,112	2.3
1_d2_NW_DI_F1_CA_7_09_5456_2	285,882	1.7
2_d2_NW_DI_F1_CA_7_09_6361_2	377,675	2.3
3_d2_NW_DI_F1_CA_7_09_6364_2	268,062	1.6
4_d2_NW_D1_F1_CA_7_09_6382_2	367,068	2.2
5_2016_TS_FT_02_d2_NW_DI_F1_CA_7_09_6385_2	113,320	0.7
6_d2_NW_DI_F1_CA_7_09_6389_2	400,863	2.4
7_dA1_NW_RC1_F2_CA_7_09_6362_2	376,622	2.3
8_dA1_NW_RC1_F2_CA_7_09_6365_2	299,860	1.8
9_d5_NW_RC1_F2_CA_7_09_6383_2	405,858	2.4
10_d5_NW_RC1_F2_CA_7_09_6386_2	326,889	2.0
11_dA1_NW_RC1_F2_CA_7_09_6390_2	330,833	2.0
12_dA3_NW_RC2_F3_CA_7_09_6363_2	325,685	2.0
13_dA3_NW_RC2_F3_CA_7_09_6366_2	291,179	1.8
14_dA3_NW_RC2_F3_CA_7_09_6384_2	383,684	2.3
15_dA3_NW_RC2_F3_CA_7_09_6388_2	292,769	1.8
16_dA3_NW_RC2_F3_CA_7_09_6391_2	289,936	1.7
A_Harbor_Seal_New_Hampshire_179629_2012_H3N8_2	392,569	2.4
pH1N1_p002_2	374,608	2.3
A_Texas_50_2012_2	413,313	2.5
BLANK_2	166.0	0.0
NEGATIVE_2	169.0	0.0
PD7_PB2_4_2	290,463	1.7
PD7_PB2_04_2	421,784	2.5

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

Sort	Visible	Group	Column	Description	ID	Scale
\|\|			Total Read Count	Total Read Count	`Total Read Count`	None
\|\|			Portion (%)	Portion (%)	`Portion (%)`	None

Sample Name	Count	Frequency (%)
TCCTTCTCTCTTTCCC	14392.0	1.5
TCCTGAGCTCTTTCCC	12773.0	1.3
GGACTCCTTCTTTCCC	11695.0	1.2
CGTACTAGTCTTTCCC	10568.0	1.1
TAAGGCGATCTTTCCC	10531.0	1.1
CTTCCTCTTCTTTCCC	9668.0	1.0
TAGGCATGTCTTTCCC	5672.0	0.6
CTTCCTCCTCTTTCCC	5640.0	0.6
AGGCAGAATCTTTCCC	5453.0	0.6
GTACTCCTTCTTTCCC	5060.0	0.5
TCCTTATCTCTTTCCC	4841.0	0.5
TCCTGCGCTCTTTCCC	4360.0	0.5
TTCCTCCTTCTTTCCC	3836.0	0.4
GTCCTCCTTCTTTCCC	3565.0	0.4
TCCTTCGCTCTTTCCC	2998.0	0.3
TCCTGATCTCTTTCCC	2889.0	0.3
CTTACTCTTCTTTCCC	2663.0	0.3
TCCTTAGCTCTTTCCC	2554.0	0.3
TCTTCCTTTCTTTCCC	2545.0	0.3
GGCCTCCTTCTTTCCC	2508.0	0.3

Sort	Visible	Group	Column	Description	ID	Scale
\|\|			Count	Count	`Count`	None
\|\|			Frequency (%)	Frequency (%)	`Frequency (%)`	None

Sample Name	Total # of Single-End Reads	Total # PF Reads	% Undetermined	% PhiX Aligned
1.0	18,111,768	16,626,017	5.8	4.1

Sort	Column	Description	ID	Scale
\|\|	Total # of Single-End Reads	Total # of Single-End Reads	`Total # of Single-End Reads`	None
\|\|	Total # PF Reads	Total # PF Reads	`Total # PF Reads`	None
\|\|	% Undetermined	% Undetermined	`% Undetermined`	None
\|\|	% PhiX Aligned	% PhiX Aligned	`% PhiX Aligned`	None

FastQC

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

Sequence Quality Histograms

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

Per Sequence Quality Scores

The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.

Per Base Sequence Content

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

Click a heatmap 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. See the FastQC help.

Per Base N Content

The percentage of base calls at each position for which an N was called. See the FastQC help.

Sequence Length Distribution

All samples have sequences of a single length (151bp).

Sequence Duplication Levels

The relative level of duplication found for every sequence. See the FastQC help.

Overrepresented sequences

The total amount of overrepresented sequences found in each library. See the FastQC help for further information.

Adapter Content

The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.

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General Statistics

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Barcodes of Undetermined Reads

Lane Statistics

FastQC

Sequence Quality Histograms

Per Sequence Quality Scores

Per Base Sequence Content

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Per Sequence GC Content

Per Base N Content

Sequence Length Distribution

Sequence Duplication Levels

Overrepresented sequences

Adapter Content

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General Statistics: Columns

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Table Qpat: Columns

Barcodes of Undetermined Reads

Table Yodk: Columns

Lane Statistics

Table Nryb: Columns

FastQC

Sequence Quality Histograms

Per Sequence Quality Scores

Per Base Sequence Content

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Per Sequence GC Content

Per Base N Content

Sequence Length Distribution

Sequence Duplication Levels

Overrepresented sequences

Adapter Content

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