MultiQC Report

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

General Statistics

Showing ⁹⁸/₉₈ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
000000000-CF4LF_l01_n01_EMP_1	89.1%	51%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_10	89.4%	53%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_11	89.2%	52%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_12	88.0%	52%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_13	87.7%	51%	251	33%	0.1
000000000-CF4LF_l01_n01_EMP_14	88.2%	52%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_15	89.6%	50%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_16	98.1%	50%	251	42%	8.9
000000000-CF4LF_l01_n01_EMP_17	91.0%	53%	251	33%	0.1
000000000-CF4LF_l01_n01_EMP_18	91.2%	52%	251	33%	0.1
000000000-CF4LF_l01_n01_EMP_19	89.6%	53%	251	33%	0.1
000000000-CF4LF_l01_n01_EMP_2	88.4%	52%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_20	91.4%	54%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_21	89.8%	52%	251	33%	0.1
000000000-CF4LF_l01_n01_EMP_22	89.1%	52%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_23	86.3%	51%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_24	87.7%	52%	251	33%	0.1
000000000-CF4LF_l01_n01_EMP_25	90.4%	49%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_26	89.2%	51%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_27	90.9%	50%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_28	90.7%	52%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_29	90.3%	50%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_3	92.6%	53%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_30	91.0%	52%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_31	89.6%	51%	251	33%	0.1
000000000-CF4LF_l01_n01_EMP_32	88.0%	49%	251	33%	0.0
000000000-CF4LF_l01_n01_EMP_33	91.9%	51%	251	42%	0.0
000000000-CF4LF_l01_n01_EMP_34	88.7%	50%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_35	90.8%	50%	251	33%	0.1
000000000-CF4LF_l01_n01_EMP_36	92.0%	52%	251	33%	0.1
000000000-CF4LF_l01_n01_EMP_37	89.5%	52%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_38	87.7%	51%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_39	88.8%	52%	251	33%	0.0
000000000-CF4LF_l01_n01_EMP_4	91.2%	53%	251	42%	0.2
000000000-CF4LF_l01_n01_EMP_40	90.5%	52%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_41	90.5%	51%	251	42%	0.0
000000000-CF4LF_l01_n01_EMP_42	90.5%	52%	251	33%	0.1
000000000-CF4LF_l01_n01_EMP_43	88.7%	51%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_44	89.9%	52%	251	33%	0.1
000000000-CF4LF_l01_n01_EMP_45	88.2%	50%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_46	91.7%	53%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_47	90.7%	51%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_48	91.5%	51%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_5	92.3%	51%	251	33%	0.3
000000000-CF4LF_l01_n01_EMP_6	93.9%	52%	251	42%	0.5
000000000-CF4LF_l01_n01_EMP_7	93.3%	51%	251	42%	0.3
000000000-CF4LF_l01_n01_EMP_8	92.1%	53%	251	42%	0.1
000000000-CF4LF_l01_n01_EMP_9	87.9%	52%	251	33%	0.1
000000000-CF4LF_l01_n01_undetermined	92.2%	46%	251	33%	2.2
000000000-CF4LF_l01_n02_EMP_1	72.6%	51%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_10	71.8%	53%	251	50%	0.1
000000000-CF4LF_l01_n02_EMP_11	71.0%	53%	251	50%	0.1
000000000-CF4LF_l01_n02_EMP_12	70.9%	52%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_13	74.0%	52%	251	42%	0.1
000000000-CF4LF_l01_n02_EMP_14	76.3%	53%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_15	73.5%	51%	251	50%	0.1
000000000-CF4LF_l01_n02_EMP_16	90.6%	52%	251	58%	8.9
000000000-CF4LF_l01_n02_EMP_17	72.6%	53%	251	50%	0.1
000000000-CF4LF_l01_n02_EMP_18	74.7%	52%	251	50%	0.1
000000000-CF4LF_l01_n02_EMP_19	70.0%	52%	251	50%	0.1
000000000-CF4LF_l01_n02_EMP_2	70.6%	53%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_20	71.2%	52%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_21	73.5%	52%	251	50%	0.1
000000000-CF4LF_l01_n02_EMP_22	72.0%	52%	251	50%	0.1
000000000-CF4LF_l01_n02_EMP_23	68.8%	51%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_24	72.6%	53%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_25	78.0%	50%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_26	75.2%	52%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_27	78.5%	53%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_28	74.0%	52%	251	42%	0.1
000000000-CF4LF_l01_n02_EMP_29	75.2%	52%	251	50%	0.1
000000000-CF4LF_l01_n02_EMP_3	76.6%	53%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_30	73.8%	52%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_31	74.2%	51%	251	50%	0.1
000000000-CF4LF_l01_n02_EMP_32	72.6%	51%	251	58%	0.0
000000000-CF4LF_l01_n02_EMP_33	78.8%	52%	251	50%	0.0
000000000-CF4LF_l01_n02_EMP_34	73.6%	51%	251	50%	0.1
000000000-CF4LF_l01_n02_EMP_35	74.7%	51%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_36	77.7%	52%	251	50%	0.1
000000000-CF4LF_l01_n02_EMP_37	72.0%	53%	251	50%	0.1
000000000-CF4LF_l01_n02_EMP_38	72.6%	53%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_39	70.6%	53%	251	58%	0.0
000000000-CF4LF_l01_n02_EMP_4	72.5%	53%	251	50%	0.2
000000000-CF4LF_l01_n02_EMP_40	73.0%	52%	251	50%	0.1
000000000-CF4LF_l01_n02_EMP_41	73.7%	52%	251	42%	0.0
000000000-CF4LF_l01_n02_EMP_42	73.7%	52%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_43	72.3%	52%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_44	71.1%	52%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_45	71.6%	51%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_46	71.6%	53%	251	42%	0.1
000000000-CF4LF_l01_n02_EMP_47	74.0%	52%	251	50%	0.1
000000000-CF4LF_l01_n02_EMP_48	75.8%	52%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_5	76.5%	51%	251	50%	0.3
000000000-CF4LF_l01_n02_EMP_6	78.1%	53%	251	50%	0.5
000000000-CF4LF_l01_n02_EMP_7	79.0%	51%	251	58%	0.3
000000000-CF4LF_l01_n02_EMP_8	74.4%	53%	251	58%	0.1
000000000-CF4LF_l01_n02_EMP_9	69.5%	53%	251	42%	0.1
000000000-CF4LF_l01_n02_undetermined	83.8%	46%	251	50%	2.2

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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

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 ⁴⁹/₄₉ rows and ²/₂ columns.

Sample Name	Total Read Count	Portion (%)
undetermined_library	2,224,667	14.1
EMP_1	64,592	0.4
EMP_2	62,051	0.4
EMP_3	118,342	0.8
EMP_4	176,402	1.1
EMP_5	265,048	1.7
EMP_6	528,985	3.4
EMP_7	339,420	2.2
EMP_8	63,968	0.4
EMP_9	67,518	0.4
EMP_10	61,490	0.4
EMP_11	64,529	0.4
EMP_12	75,741	0.5
EMP_13	137,576	0.9
EMP_14	63,436	0.4
EMP_15	95,826	0.6
EMP_16	8,941,946	56.8
EMP_17	66,284	0.4
EMP_18	112,227	0.7
EMP_19	86,421	0.5
EMP_20	62,331	0.4
EMP_21	106,739	0.7
EMP_22	104,235	0.7
EMP_23	90,212	0.6
EMP_24	67,446	0.4
EMP_25	90,247	0.6
EMP_26	59,196	0.4
EMP_27	101,908	0.6
EMP_28	69,396	0.4
EMP_29	84,388	0.5
EMP_30	74,392	0.5
EMP_31	76,396	0.5
EMP_32	39,181	0.2
EMP_33	42,166	0.3
EMP_34	82,071	0.5
EMP_35	95,797	0.6
EMP_36	80,864	0.5
EMP_37	65,136	0.4
EMP_38	77,164	0.5
EMP_39	39,767	0.3
EMP_40	75,680	0.5
EMP_41	42,964	0.3
EMP_42	55,809	0.4
EMP_43	78,027	0.5
EMP_44	70,770	0.4
EMP_45	83,182	0.5
EMP_46	61,904	0.4
EMP_47	82,233	0.5
EMP_48	80,421	0.5

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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 (%)
TTCCTTCTTCTT	14799.0	0.7
TTCCTTATTCTT	10087.0	0.5
TTCCTTCTTCGT	8157.0	0.4
TTCCTTCGTCTT	6710.0	0.3
TTCCTTCTTATT	5499.0	0.2
TTCTTAGTAGTT	4935.0	0.2
CTTGTAATCTCG	4734.0	0.2
GCCAATATCTCG	4639.0	0.2
TGACCAATCTCG	4304.0	0.2
TTCCTTATCTGT	4275.0	0.2
ACAGTGATCTCG	4018.0	0.2
TCCTTAGTAGTT	3770.0	0.2
CAGATCATCTCG	3578.0	0.2
CGATGTATCTCG	3446.0	0.1
TTCCTTACTCTT	3438.0	0.1
TTCCTTGTAGTT	3377.0	0.1
TTCCTAGTAGTT	3295.0	0.1
TTCCTTCTACTT	3228.0	0.1
TTCCTTCCTCTT	2935.0	0.1
TTCCTTATTCAT	2896.0	0.1

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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	23,157,820	15,756,491	14.1	12.6

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 (251bp).

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.

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

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General Statistics

Lane 1 Demultiplexing Report

Barcodes of Undetermined Reads

Lane Statistics

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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General Statistics

General Statistics: Columns

Lane 1 Demultiplexing Report

Table Hiwf: Columns

Barcodes of Undetermined Reads

Table Dqbp: Columns

Lane Statistics

Table Hrke: 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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