MultiQC Report

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

General Statistics

Showing ¹²²/₁₂₂ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
000000000-J3T7H_l01_n01_A10_AR	82.6%	39%	151	25%	0.3
000000000-J3T7H_l01_n01_A11_AR	86.4%	39%	151	25%	0.2
000000000-J3T7H_l01_n01_A12_AR	84.1%	40%	151	33%	0.2
000000000-J3T7H_l01_n01_A1_AR	63.1%	42%	151	25%	0.2
000000000-J3T7H_l01_n01_A2_AR	84.1%	43%	151	17%	0.3
000000000-J3T7H_l01_n01_A3_AR	82.2%	43%	151	17%	0.2
000000000-J3T7H_l01_n01_A4_AR	58.5%	44%	151	25%	0.3
000000000-J3T7H_l01_n01_A5_AR	85.2%	44%	151	17%	0.2
000000000-J3T7H_l01_n01_A6_AR	82.6%	43%	151	25%	0.3
000000000-J3T7H_l01_n01_A7_AR	71.2%	45%	151	33%	0.3
000000000-J3T7H_l01_n01_A8_AR	84.2%	40%	151	25%	0.2
000000000-J3T7H_l01_n01_A9_AR	82.0%	39%	151	25%	0.2
000000000-J3T7H_l01_n01_B10_AR	71.8%	43%	151	33%	0.2
000000000-J3T7H_l01_n01_B11_AR	81.5%	39%	151	25%	0.1
000000000-J3T7H_l01_n01_B12_AR	82.9%	41%	151	33%	0.2
000000000-J3T7H_l01_n01_B1_AR	52.4%	42%	151	33%	0.2
000000000-J3T7H_l01_n01_B2_AR	66.7%	43%	151	25%	0.0
000000000-J3T7H_l01_n01_B3_AR	84.0%	43%	151	25%	0.2
000000000-J3T7H_l01_n01_B4_AR	57.7%	45%	151	33%	0.0
000000000-J3T7H_l01_n01_B5_AR	78.7%	40%	151	17%	0.1
000000000-J3T7H_l01_n01_B6_AR	71.2%	40%	151	33%	0.1
000000000-J3T7H_l01_n01_B7_AR	69.6%	46%	151	25%	0.2
000000000-J3T7H_l01_n01_B8_AR	85.7%	40%	151	25%	0.2
000000000-J3T7H_l01_n01_B9_AR	84.9%	39%	151	33%	0.2
000000000-J3T7H_l01_n01_C10_AR	86.5%	40%	151	25%	0.2
000000000-J3T7H_l01_n01_C11_AR	70.1%	45%	151	33%	0.2
000000000-J3T7H_l01_n01_C12_AR	78.9%	40%	151	25%	0.1
000000000-J3T7H_l01_n01_C1_AR	71.4%	44%	151	25%	0.1
000000000-J3T7H_l01_n01_C2_AR	82.4%	44%	151	25%	0.2
000000000-J3T7H_l01_n01_C3_AR	81.8%	43%	151	17%	0.2
000000000-J3T7H_l01_n01_C4_AR	71.7%	46%	151	42%	0.2
000000000-J3T7H_l01_n01_C5_AR	83.9%	40%	151	17%	0.2
000000000-J3T7H_l01_n01_C6_AR	81.8%	39%	151	17%	0.2
000000000-J3T7H_l01_n01_C7_AR	71.9%	47%	151	25%	0.2
000000000-J3T7H_l01_n01_C8_AR	82.6%	40%	151	25%	0.2
000000000-J3T7H_l01_n01_C9_AR	83.2%	39%	151	33%	0.2
000000000-J3T7H_l01_n01_D10_AR	83.5%	40%	151	25%	0.2
000000000-J3T7H_l01_n01_D11_AR	65.1%	45%	151	33%	0.1
000000000-J3T7H_l01_n01_D12_AR	80.6%	40%	151	25%	0.1
000000000-J3T7H_l01_n01_D1_AR	49.0%	43%	151	25%	0.2
000000000-J3T7H_l01_n01_D2_AR	84.8%	44%	151	17%	0.3
000000000-J3T7H_l01_n01_D3_AR	82.9%	44%	151	33%	0.2
000000000-J3T7H_l01_n01_D4_AR	73.1%	48%	151	25%	0.2
000000000-J3T7H_l01_n01_D5_AR	84.5%	40%	151	25%	0.2
000000000-J3T7H_l01_n01_D6_AR	84.8%	40%	151	33%	0.2
000000000-J3T7H_l01_n01_D7_AR	69.3%	48%	151	25%	0.2
000000000-J3T7H_l01_n01_D8_AR	84.5%	41%	151	25%	0.2
000000000-J3T7H_l01_n01_D9_AR	84.2%	40%	151	33%	0.2
000000000-J3T7H_l01_n01_E10_AR	77.4%	40%	151	17%	0.1
000000000-J3T7H_l01_n01_E11_AR	65.7%	45%	151	25%	0.2
000000000-J3T7H_l01_n01_E12_AR	83.8%	40%	151	25%	0.2
000000000-J3T7H_l01_n01_E1_AR	48.0%	43%	151	8%	0.2
000000000-J3T7H_l01_n01_E2_AR	84.6%	44%	151	17%	0.3
000000000-J3T7H_l01_n01_E3_AR	81.9%	43%	151	33%	0.2
000000000-J3T7H_l01_n01_E4_AR	70.3%	48%	151	25%	0.2
000000000-J3T7H_l01_n01_E5_AR	82.6%	41%	151	25%	0.2
000000000-J3T7H_l01_n01_E6_AR	82.4%	40%	151	17%	0.2
000000000-J3T7H_l01_n01_E7_AR	67.5%	47%	151	25%	0.2
000000000-J3T7H_l01_n01_E8_AR	83.0%	41%	151	17%	0.2
000000000-J3T7H_l01_n01_E9_AR	80.4%	41%	151	17%	0.1
000000000-J3T7H_l01_n01_undetermined	58.4%	42%	151	17%	0.3
000000000-J3T7H_l01_n02_A10_AR	81.6%	39%	151	33%	0.3
000000000-J3T7H_l01_n02_A11_AR	85.5%	39%	151	33%	0.2
000000000-J3T7H_l01_n02_A12_AR	83.5%	40%	151	33%	0.2
000000000-J3T7H_l01_n02_A1_AR	62.3%	42%	151	25%	0.2
000000000-J3T7H_l01_n02_A2_AR	82.3%	43%	151	17%	0.3
000000000-J3T7H_l01_n02_A3_AR	78.8%	43%	151	17%	0.2
000000000-J3T7H_l01_n02_A4_AR	58.1%	44%	151	33%	0.3
000000000-J3T7H_l01_n02_A5_AR	83.8%	44%	151	17%	0.2
000000000-J3T7H_l01_n02_A6_AR	81.5%	43%	151	25%	0.3
000000000-J3T7H_l01_n02_A7_AR	69.8%	45%	151	33%	0.3
000000000-J3T7H_l01_n02_A8_AR	83.9%	40%	151	33%	0.2
000000000-J3T7H_l01_n02_A9_AR	82.3%	39%	151	25%	0.2
000000000-J3T7H_l01_n02_B10_AR	70.7%	43%	151	33%	0.2
000000000-J3T7H_l01_n02_B11_AR	80.5%	39%	151	25%	0.1
000000000-J3T7H_l01_n02_B12_AR	82.6%	41%	151	33%	0.2
000000000-J3T7H_l01_n02_B1_AR	51.7%	42%	151	25%	0.2
000000000-J3T7H_l01_n02_B2_AR	64.3%	43%	151	25%	0.0
000000000-J3T7H_l01_n02_B3_AR	80.7%	43%	151	25%	0.2
000000000-J3T7H_l01_n02_B4_AR	48.8%	46%	151	25%	0.0
000000000-J3T7H_l01_n02_B5_AR	75.0%	40%	151	17%	0.1
000000000-J3T7H_l01_n02_B6_AR	70.1%	40%	151	25%	0.1
000000000-J3T7H_l01_n02_B7_AR	69.3%	46%	151	25%	0.2
000000000-J3T7H_l01_n02_B8_AR	84.0%	40%	151	25%	0.2
000000000-J3T7H_l01_n02_B9_AR	84.0%	39%	151	25%	0.2
000000000-J3T7H_l01_n02_C10_AR	86.5%	40%	151	25%	0.2
000000000-J3T7H_l01_n02_C11_AR	70.5%	45%	151	42%	0.2
000000000-J3T7H_l01_n02_C12_AR	79.1%	40%	151	25%	0.1
000000000-J3T7H_l01_n02_C1_AR	73.2%	44%	151	25%	0.1
000000000-J3T7H_l01_n02_C2_AR	82.2%	44%	151	17%	0.2
000000000-J3T7H_l01_n02_C3_AR	78.7%	43%	151	25%	0.2
000000000-J3T7H_l01_n02_C4_AR	71.9%	46%	151	33%	0.2
000000000-J3T7H_l01_n02_C5_AR	83.6%	40%	151	25%	0.2
000000000-J3T7H_l01_n02_C6_AR	82.8%	39%	151	8%	0.2
000000000-J3T7H_l01_n02_C7_AR	72.4%	47%	151	25%	0.2
000000000-J3T7H_l01_n02_C8_AR	82.5%	40%	151	25%	0.2
000000000-J3T7H_l01_n02_C9_AR	83.4%	40%	151	33%	0.2
000000000-J3T7H_l01_n02_D10_AR	83.3%	40%	151	25%	0.2
000000000-J3T7H_l01_n02_D11_AR	65.2%	45%	151	33%	0.1
000000000-J3T7H_l01_n02_D12_AR	79.8%	40%	151	25%	0.1
000000000-J3T7H_l01_n02_D1_AR	48.7%	43%	151	25%	0.2
000000000-J3T7H_l01_n02_D2_AR	82.8%	44%	151	17%	0.3
000000000-J3T7H_l01_n02_D3_AR	79.6%	44%	151	42%	0.2
000000000-J3T7H_l01_n02_D4_AR	72.4%	48%	151	25%	0.2
000000000-J3T7H_l01_n02_D5_AR	84.3%	40%	151	25%	0.2
000000000-J3T7H_l01_n02_D6_AR	83.8%	40%	151	25%	0.2
000000000-J3T7H_l01_n02_D7_AR	68.5%	48%	151	25%	0.2
000000000-J3T7H_l01_n02_D8_AR	82.8%	41%	151	25%	0.2
000000000-J3T7H_l01_n02_D9_AR	83.2%	40%	151	33%	0.2
000000000-J3T7H_l01_n02_E10_AR	79.0%	40%	151	17%	0.1
000000000-J3T7H_l01_n02_E11_AR	64.2%	45%	151	25%	0.2
000000000-J3T7H_l01_n02_E12_AR	81.9%	40%	151	25%	0.2
000000000-J3T7H_l01_n02_E1_AR	47.3%	43%	151	17%	0.2
000000000-J3T7H_l01_n02_E2_AR	82.3%	44%	151	17%	0.3
000000000-J3T7H_l01_n02_E3_AR	77.9%	43%	151	25%	0.2
000000000-J3T7H_l01_n02_E4_AR	69.2%	48%	151	17%	0.2
000000000-J3T7H_l01_n02_E5_AR	81.0%	41%	151	25%	0.2
000000000-J3T7H_l01_n02_E6_AR	80.4%	40%	151	8%	0.2
000000000-J3T7H_l01_n02_E7_AR	66.1%	47%	151	33%	0.2
000000000-J3T7H_l01_n02_E8_AR	81.2%	41%	151	17%	0.2
000000000-J3T7H_l01_n02_E9_AR	78.7%	41%	151	25%	0.1
000000000-J3T7H_l01_n02_undetermined	53.8%	42%	151	17%	0.3

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 ⁶¹/₆₁ rows and ²/₂ columns.

Sample Name	Total Read Count	Portion (%)
undetermined_library	286,866	2.5
A1_AR	210,131	1.8
B1_AR	161,544	1.4
C1_AR	128,369	1.1
D1_AR	196,778	1.7
E1_AR	193,901	1.7
A2_AR	259,188	2.2
B2_AR	46,489	0.4
C2_AR	201,861	1.7
D2_AR	251,460	2.2
E2_AR	292,912	2.5
A3_AR	205,583	1.8
B3_AR	216,340	1.9
C3_AR	189,959	1.6
D3_AR	202,653	1.7
E3_AR	218,008	1.9
A4_AR	252,167	2.2
B4_AR	45,986	0.4
C4_AR	230,045	2.0
D4_AR	208,354	1.8
E4_AR	176,908	1.5
A5_AR	238,412	2.0
B5_AR	89,447	0.8
C5_AR	166,692	1.4
D5_AR	207,229	1.8
E5_AR	170,391	1.5
A6_AR	261,520	2.2
B6_AR	73,936	0.6
C6_AR	158,127	1.4
D6_AR	216,780	1.9
E6_AR	162,427	1.4
A7_AR	261,792	2.2
B7_AR	218,020	1.9
C7_AR	184,891	1.6
D7_AR	181,354	1.6
E7_AR	218,675	1.9
A8_AR	235,582	2.0
B8_AR	207,191	1.8
C8_AR	168,791	1.4
D8_AR	199,133	1.7
E8_AR	222,224	1.9
A9_AR	204,770	1.8
B9_AR	203,574	1.7
C9_AR	164,502	1.4
D9_AR	186,929	1.6
E9_AR	117,963	1.0
A10_AR	311,353	2.7
B10_AR	206,088	1.8
C10_AR	249,646	2.1
D10_AR	173,294	1.5
E10_AR	111,812	1.0
A11_AR	239,665	2.1
B11_AR	115,472	1.0
C11_AR	182,794	1.6
D11_AR	141,197	1.2
E11_AR	191,456	1.6
A12_AR	216,416	1.9
B12_AR	158,700	1.4
C12_AR	140,313	1.2
D12_AR	136,099	1.2
E12_AR	184,698	1.6

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 (%)
CGAGGCTGACTGCATA	8664.0	3.0
AGGCAGAAGTAAGGAG	8659.0	3.0
CGTACTAGGTAAGGAG	8640.0	3.0
AGGCAGAAACTGCATA	8094.0	2.8
AGGCAGAATATCCTCT	7154.0	2.5
CTCTCTACACTGCATA	6754.0	2.4
CTCTCTACTATCCTCT	6605.0	2.3
CGAGGCTGTATCCTCT	6550.0	2.3
ATCTCAGGTATCCTCT	6180.0	2.1
CGTACTAGTATCCTCT	4582.0	1.6
CTCTCTACGTAAGGAG	2846.0	1.0
CGAGGCTGGTAAGGAG	2712.0	0.9
CGTACTAGACTGCATA	1027.0	0.4
TTTTTTTTTTTTTTTT	968.0	0.3
TCCTTCTCTCTTTCCC	597.0	0.2
GTAGAGGATAAGCCTT	521.0	0.2
CGTACTAGTAAGCCTT	504.0	0.2
TCCTGAGCTAAGCCTT	493.0	0.2
AGGCAGAATAAGCCTT	490.0	0.2
GTACTAGATCTCTCCG	454.0	0.2

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	12,365,743	11,654,857	2.5	0.7

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.

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. See the FastQC help.

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. 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.

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. See the FastQC help.

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

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.

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. See the FastQC help for further information.

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. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.

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

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About MultiQC

General Statistics

Lane 1 Demultiplexing Report

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

General Statistics: Columns

Lane 1 Demultiplexing Report

Table Numz: Columns

Barcodes of Undetermined Reads

Table Iobh: Columns

Lane Statistics

Table Yhbf: Columns

FastQC

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

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