MultiQC Report

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

General Statistics

Showing ⁶⁴/₆₄ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
HTW7MBGXG_n01_PpBSD_Pp-B_r1	43.5%	36%	76	17%	10.5
HTW7MBGXG_n01_PpBSD_Pp-B_r2	50.4%	36%	76	25%	18.3
HTW7MBGXG_n01_SPL16_Colamp-B_r	49.6%	36%	76	8%	8.3
HTW7MBGXG_n01_TGA5_Col-B_ryq269	12.6%	38%	76	17%	0.0
HTW7MBGXG_n01_TGA5_Colamp-B_ryq269	47.1%	38%	76	17%	5.2
HTW7MBGXG_n01_VvHY5_CS8amp-B_r	39.2%	40%	76	8%	117.9
HTW7MBGXG_n01_VvHY5_PN94amp-B_r	24.8%	40%	76	8%	137.3
HTW7MBGXG_n01_VvMYB135_PN94-B_r1	38.3%	38%	76	8%	19.1
HTW7MBGXG_n01_VvMYB135_PN94-B_r2	44.6%	37%	76	8%	42.4
HTW7MBGXG_n01_VvMYB13_PN94-B_r1	38.8%	38%	76	17%	37.0
HTW7MBGXG_n01_VvMYB13_PN94-B_r2	40.9%	38%	76	17%	21.3
HTW7MBGXG_n01_bZIP25C_Col-B_r	27.5%	37%	76	8%	0.2
HTW7MBGXG_n01_bZIP63_Col-B_r	30.9%	37%	76	17%	0.4
HTW7MBGXG_n01_daplib_Col-input_ryq269	16.9%	36%	76	17%	0.9
HTW7MBGXG_n01_daplib_poolR1_ryq269	17.1%	37%	76	17%	5.3
HTW7MBGXG_n01_daplib_poolR2_ryq269	22.2%	37%	76	17%	3.8
HTW7MBGXG_n01_daplib_poolR3_ryq269	29.7%	37%	76	17%	2.1
HTW7MBGXG_n01_daplib_poolR4_ryq269	13.7%	37%	76	17%	5.9
HTW7MBGXG_n01_daplib_poolR5_ryq269	18.3%	37%	76	17%	3.9
HTW7MBGXG_n01_daplib_poolR6_ryq269	23.3%	37%	76	17%	2.6
HTW7MBGXG_n01_daplib_poolR7_ryq269	36.2%	37%	76	17%	6.7
HTW7MBGXG_n01_pIXHALOC_Col-B_r	28.1%	37%	76	17%	0.3
HTW7MBGXG_n01_pIXHALO_Col-B_r	33.0%	36%	76	0%	0.2
HTW7MBGXG_n01_pIXHALO_Col-B_ryq269	15.5%	36%	76	17%	0.0
HTW7MBGXG_n01_pIXHALO_Colamp-B_ryq269	28.3%	36%	76	17%	1.2
HTW7MBGXG_n01_pIXHALO_PN94-B_r1	22.0%	38%	76	8%	8.4
HTW7MBGXG_n01_pIXHALO_PN94-B_r2	22.3%	39%	76	8%	6.6
HTW7MBGXG_n01_ps-bZIP1..ph..bZIP25C_Col..h_B_r1	33.2%	37%	76	8%	0.9
HTW7MBGXG_n01_ps-bZIP1..ph..bZIP25C_Col..h_B_r2	38.2%	37%	76	8%	1.1
HTW7MBGXG_n01_ps-bZIP10..ph-bZIP11_Col..s-B..h-B_r	41.2%	41%	76	8%	7.3
HTW7MBGXG_n01_ps-bZIP10..ph-bZIP9_Col..h-B_q_2	52.6%	36%	76	17%	1.6
HTW7MBGXG_n01_ps-bZIP10..ph-vec_Col..h_B_q_2	34.8%	37%	76	8%	0.2
HTW7MBGXG_n01_ps-bZIP11..ph-bZIP10_Col..s-B..h-B_r	41.5%	39%	76	8%	0.2
HTW7MBGXG_n01_ps-bZIP11..ph..bZIP25C_Col..h_B_r1	40.1%	37%	76	17%	1.0
HTW7MBGXG_n01_ps-bZIP11..ph..bZIP25C_Col..h_B_r2	40.0%	38%	76	17%	1.0
HTW7MBGXG_n01_ps-bZIP2..ph-bZIP10_Col..h-B_r1	49.2%	41%	76	8%	13.7
HTW7MBGXG_n01_ps-bZIP2..ph-bZIP10_Col..h-B_r2	53.4%	41%	76	17%	20.1
HTW7MBGXG_n01_ps-bZIP2..ph-bZIP63_Col..h-B_r1	27.7%	41%	76	17%	0.4
HTW7MBGXG_n01_ps-bZIP2..ph-bZIP63_Col..h-B_r2	46.6%	40%	76	17%	1.5
HTW7MBGXG_n01_ps-bZIP2..ph-bZIP9_Col..h-B_r1	56.7%	42%	76	17%	5.9
HTW7MBGXG_n01_ps-bZIP2..ph-bZIP9_Col..h-B_r2	58.1%	42%	76	17%	8.9
HTW7MBGXG_n01_ps-bZIP2..ph..bZIP25C_Col..h_B_r1	40.6%	38%	76	8%	0.5
HTW7MBGXG_n01_ps-bZIP2..ph..bZIP25C_Col..h_B_r2	41.6%	38%	76	8%	1.1
HTW7MBGXG_n01_ps-bZIP25..ph-bZIP9_Col..h-B_q_2	52.2%	36%	76	17%	2.3
HTW7MBGXG_n01_ps-bZIP25..ph-vec_Col..h_B_q_2	37.1%	37%	76	0%	0.2
HTW7MBGXG_n01_ps-bZIP44..ph..bZIP25C_Col..h_B_r1	37.1%	38%	76	17%	0.8
HTW7MBGXG_n01_ps-bZIP44..ph..bZIP25C_Col..h_B_r2	44.2%	37%	76	17%	1.2
HTW7MBGXG_n01_ps-bZIP53..ph-bZIP10_Col..h-B_q_2	34.6%	36%	76	0%	0.7
HTW7MBGXG_n01_ps-bZIP53..ph-bZIP25_Col..h-B_q1_2	28.0%	36%	76	8%	0.8
HTW7MBGXG_n01_ps-bZIP53..ph-bZIP25_Col..h-B_q2_2	31.3%	37%	76	0%	0.9
HTW7MBGXG_n01_ps-bZIP53..ph-bZIP9_Col..h-B_q_2	36.3%	36%	76	8%	1.1
HTW7MBGXG_n01_ps-bZIP53..ph..bZIP25C_Col..h_B_r1	44.7%	38%	76	17%	1.8
HTW7MBGXG_n01_ps-bZIP53..ph..bZIP25C_Col..h_B_r2	42.1%	38%	76	17%	1.8
HTW7MBGXG_n01_ps-bZIP63..ph-bZIP9_Col..h-B_q_2	56.2%	36%	76	17%	1.7
HTW7MBGXG_n01_ps-bZIP63..ph-vec_Col..h_B_q_2	47.3%	36%	76	8%	0.3
HTW7MBGXG_n01_ps-bZIP9..ph-bZIP10_Col..h-B_q_2	56.5%	37%	76	17%	2.2
HTW7MBGXG_n01_ps-bZIP9..ph-bZIP25_Col..h-B_q_2	53.7%	36%	76	17%	2.1
HTW7MBGXG_n01_ps-bZIP9..ph-bZIP63_Col..h-B_q_2	24.7%	37%	76	8%	0.5
HTW7MBGXG_n01_ps-bZIP9..ph-vec_Col..h_B_q_2	56.1%	36%	76	17%	0.4
HTW7MBGXG_n01_ps-vec..ph..bZIP25C_Col..h_B_r1	32.8%	37%	76	8%	0.4
HTW7MBGXG_n01_ps-vec..ph..bZIP25C_Col..h_B_r2	38.6%	37%	76	8%	0.6
HTW7MBGXG_n01_ps-vec..ph..bZIP63_Col..h_B_r1	33.6%	37%	76	8%	0.4
HTW7MBGXG_n01_ps-vec..ph..bZIP63_Col..h_B_r2	39.9%	37%	76	8%	0.6
HTW7MBGXG_n01_undetermined	54.4%	42%	76	25%	48.0

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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

Demultiplexing Report

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 ⁶⁴/₆₄ rows and ²/₂ columns.

Sample Name	Total Read Count	Portion (%)
undetermined_library	47,994,633	8.0
VvHY5_CS8amp-B_r	117,929,759	19.7
VvHY5_PN94amp-B_r	137,307,470	22.9
pIXHALO_PN94-B_r1	8,399,801	1.4
pIXHALO_PN94-B_r2	6,612,998	1.1
VvMYB13_PN94-B_r1	36,980,166	6.2
VvMYB13_PN94-B_r2	21,345,433	3.6
VvMYB135_PN94-B_r1	19,089,533	3.2
VvMYB135_PN94-B_r2	42,449,854	7.1
pIXHALO_Col-B_r	212,140	0.0
SPL16_Colamp-B_r	8,321,063	1.4
pIXHALOC_Col-B_r	275,497	0.0
bZIP25C_Col-B_r	176,321	0.0
bZIP63_Col-B_r	422,461	0.1
PpBSD_Pp-B_r1	10,500,244	1.8
PpBSD_Pp-B_r2	18,318,976	3.1
ps-bZIP10..ph-bZIP11_Col..s-B..h-B_r	7,270,150	1.2
ps-bZIP11..ph-bZIP10_Col..s-B..h-B_r	221,038	0.0
ps-vec..ph..bZIP63_Col..h_B_r1	423,974	0.1
ps-vec..ph..bZIP63_Col..h_B_r2	581,202	0.1
ps-vec..ph..bZIP25C_Col..h_B_r1	434,823	0.1
ps-vec..ph..bZIP25C_Col..h_B_r2	614,725	0.1
ps-bZIP1..ph..bZIP25C_Col..h_B_r1	869,604	0.1
ps-bZIP1..ph..bZIP25C_Col..h_B_r2	1,085,307	0.2
ps-bZIP2..ph..bZIP25C_Col..h_B_r1	461,071	0.1
ps-bZIP2..ph..bZIP25C_Col..h_B_r2	1,054,012	0.2
ps-bZIP11..ph..bZIP25C_Col..h_B_r1	971,885	0.2
ps-bZIP11..ph..bZIP25C_Col..h_B_r2	981,509	0.2
ps-bZIP44..ph..bZIP25C_Col..h_B_r1	756,703	0.1
ps-bZIP44..ph..bZIP25C_Col..h_B_r2	1,192,297	0.2
ps-bZIP53..ph..bZIP25C_Col..h_B_r1	1,838,620	0.3
ps-bZIP53..ph..bZIP25C_Col..h_B_r2	1,832,481	0.3
ps-bZIP2..ph-bZIP9_Col..h-B_r1	5,910,355	1.0
ps-bZIP2..ph-bZIP9_Col..h-B_r2	8,864,894	1.5
ps-bZIP2..ph-bZIP10_Col..h-B_r1	13,709,666	2.3
ps-bZIP2..ph-bZIP10_Col..h-B_r2	20,072,064	3.3
ps-bZIP2..ph-bZIP63_Col..h-B_r1	364,142	0.1
ps-bZIP2..ph-bZIP63_Col..h-B_r2	1,527,210	0.3
ps-bZIP53..ph-bZIP25_Col..h-B_q1_2	831,252	0.1
ps-bZIP53..ph-bZIP25_Col..h-B_q2_2	914,729	0.2
ps-bZIP53..ph-bZIP9_Col..h-B_q_2	1,134,904	0.2
ps-bZIP53..ph-bZIP10_Col..h-B_q_2	670,387	0.1
ps-bZIP9..ph-bZIP10_Col..h-B_q_2	2,218,290	0.4
ps-bZIP9..ph-bZIP25_Col..h-B_q_2	2,107,785	0.4
ps-bZIP9..ph-bZIP63_Col..h-B_q_2	464,964	0.1
ps-bZIP10..ph-bZIP9_Col..h-B_q_2	1,603,790	0.3
ps-bZIP25..ph-bZIP9_Col..h-B_q_2	2,298,471	0.4
ps-bZIP63..ph-bZIP9_Col..h-B_q_2	1,699,376	0.3
ps-bZIP63..ph-vec_Col..h_B_q_2	308,862	0.1
ps-bZIP9..ph-vec_Col..h_B_q_2	423,603	0.1
ps-bZIP10..ph-vec_Col..h_B_q_2	248,260	0.0
ps-bZIP25..ph-vec_Col..h_B_q_2	240,619	0.0
pIXHALO_Colamp-B_ryq269	1,171,498	0.2
TGA5_Colamp-B_ryq269	5,205,035	0.9
pIXHALO_Col-B_ryq269	10,075	0.0
TGA5_Col-B_ryq269	32,219	0.0
daplib_Col-input_ryq269	878,825	0.1
daplib_poolR1_ryq269	5,294,228	0.9
daplib_poolR2_ryq269	3,791,361	0.6
daplib_poolR3_ryq269	2,143,660	0.4
daplib_poolR4_ryq269	5,876,905	1.0
daplib_poolR5_ryq269	3,851,745	0.6
daplib_poolR6_ryq269	2,550,884	0.4
daplib_poolR7_ryq269	6,732,314	1.1

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

Barcodes of Undetermined Reads

Barcodes of Undetermined Reads
We have determined the barcodes of your undetermined reads (reads containing a barcode that you did not encode in your metadata). Here are the top 20 barcodes belonging to the undetermined reads. The full list is available here.

Showing ²⁰/₂₀ rows and ²/₂ columns.

Sample Name	Count	Frequency (%)
GGGGGGGGAGATCTCG	22012744.0	45.9
TAATGCGCGGGGGGGG	1430380.0	3.0
TAATGCGCAGATAGGG	876231.0	1.8
GGGGGGGGTAAGATTA	575198.0	1.2
GGGGGGGGAGGATAGG	515789.0	1.1
GGGGGGGGAGCTCTCG	489386.0	1.0
TAATGCGCAAAAAATA	381336.0	0.8
CGCTCATTGGGGGGGG	375344.0	0.8
TAATCGCATAAGATTA	302369.0	0.6
TAATCGCAAGGATAGG	292943.0	0.6
TAATGCGCAAGATTAG	266736.0	0.6
CTGAAGCTGGGGGGGG	230029.0	0.5
TAATGCCATAAGATTA	204758.0	0.4
TCTCGCGCGGGGGGGG	204670.0	0.4
TAATGCCAAGGATAGG	200161.0	0.4
TAATGCGCAAACAATA	187419.0	0.4
TAATGCGCAAAGAATA	186599.0	0.4
TAAGCGCATAAGATTA	175673.0	0.4
TAATGCGCATGATAGT	165623.0	0.3
TAATGCGCAGGAAGGG	164764.0	0.3

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

Run Statistics

Showing ¹/₁ rows and ⁴/₄ columns.

Sample Name	Total # of Single-End Reads	Total # PF Reads	% Undetermined	% PhiX Aligned
4.0	747,324,208	600,078,122	8.0	3.9

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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 (76bp).

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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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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Table Jxnv: Columns

Run Statistics

Table Czif: 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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