MultiQC Report

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

General Statistics

Showing ⁹⁵/₉₅ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
HWCTGDRXX_n01_C1_1	56.7%	50%	76	50%	12.4
HWCTGDRXX_n01_C1_100	63.9%	50%	76	50%	17.8
HWCTGDRXX_n01_C1_108	66.8%	49%	76	50%	21.3
HWCTGDRXX_n01_C1_11	50.1%	48%	76	42%	13.5
HWCTGDRXX_n01_C1_118	52.4%	49%	76	42%	13.9
HWCTGDRXX_n01_C1_124	58.9%	50%	76	50%	14.4
HWCTGDRXX_n01_C1_125	57.3%	49%	76	50%	18.8
HWCTGDRXX_n01_C1_126	55.2%	49%	76	42%	19.4
HWCTGDRXX_n01_C1_135	50.5%	49%	76	42%	19.5
HWCTGDRXX_n01_C1_139	12.7%	49%	76	17%	0.3
HWCTGDRXX_n01_C1_14	51.3%	48%	76	33%	23.7
HWCTGDRXX_n01_C1_146	55.9%	49%	76	42%	20.7
HWCTGDRXX_n01_C1_148	55.5%	48%	76	42%	19.0
HWCTGDRXX_n01_C1_149	51.4%	48%	76	33%	20.4
HWCTGDRXX_n01_C1_155	54.8%	49%	76	42%	24.7
HWCTGDRXX_n01_C1_162	60.3%	50%	76	50%	21.3
HWCTGDRXX_n01_C1_169	56.4%	49%	76	50%	10.5
HWCTGDRXX_n01_C1_170	63.1%	49%	76	50%	24.4
HWCTGDRXX_n01_C1_177	61.5%	49%	76	42%	22.1
HWCTGDRXX_n01_C1_185	20.9%	48%	76	25%	1.0
HWCTGDRXX_n01_C1_208	52.5%	49%	76	42%	18.9
HWCTGDRXX_n01_C1_209	54.0%	49%	76	50%	17.6
HWCTGDRXX_n01_C1_213	52.6%	48%	76	42%	22.8
HWCTGDRXX_n01_C1_215	52.7%	49%	76	42%	17.5
HWCTGDRXX_n01_C1_22	59.9%	49%	76	50%	24.1
HWCTGDRXX_n01_C1_220	54.5%	49%	76	50%	16.7
HWCTGDRXX_n01_C1_221	50.9%	48%	76	33%	16.5
HWCTGDRXX_n01_C1_225	58.7%	50%	76	33%	26.7
HWCTGDRXX_n01_C1_227	59.0%	49%	76	42%	24.8
HWCTGDRXX_n01_C1_246	58.0%	50%	76	33%	14.7
HWCTGDRXX_n01_C1_253	56.7%	50%	76	33%	29.9
HWCTGDRXX_n01_C1_262	64.5%	50%	76	42%	27.5
HWCTGDRXX_n01_C1_264	58.7%	50%	76	50%	23.5
HWCTGDRXX_n01_C1_269	52.6%	49%	76	42%	18.6
HWCTGDRXX_n01_C1_270	57.0%	49%	76	42%	22.5
HWCTGDRXX_n01_C1_275	54.0%	48%	76	42%	28.0
HWCTGDRXX_n01_C1_278	56.5%	49%	76	33%	21.2
HWCTGDRXX_n01_C1_279	50.2%	48%	76	42%	14.8
HWCTGDRXX_n01_C1_280	51.6%	49%	76	33%	21.7
HWCTGDRXX_n01_C1_281	55.1%	49%	76	33%	22.8
HWCTGDRXX_n01_C1_286	60.1%	50%	76	42%	19.6
HWCTGDRXX_n01_C1_287	55.4%	50%	76	42%	18.1
HWCTGDRXX_n01_C1_290	61.6%	50%	76	33%	59.2
HWCTGDRXX_n01_C1_296	64.1%	49%	76	33%	29.1
HWCTGDRXX_n01_C1_297	50.7%	48%	76	33%	16.7
HWCTGDRXX_n01_C1_298	56.6%	48%	76	33%	26.8
HWCTGDRXX_n01_C1_302	54.2%	49%	76	33%	23.6
HWCTGDRXX_n01_C1_304	54.1%	49%	76	42%	31.8
HWCTGDRXX_n01_C1_311	52.3%	49%	76	33%	20.4
HWCTGDRXX_n01_C1_313	52.5%	48%	76	42%	18.0
HWCTGDRXX_n01_C1_314	52.6%	49%	76	33%	21.9
HWCTGDRXX_n01_C1_317	52.4%	49%	76	33%	22.2
HWCTGDRXX_n01_C1_318	61.1%	50%	76	42%	27.8
HWCTGDRXX_n01_C1_319	52.1%	49%	76	33%	18.9
HWCTGDRXX_n01_C1_321	55.9%	49%	76	33%	34.0
HWCTGDRXX_n01_C1_324	58.0%	49%	76	42%	24.3
HWCTGDRXX_n01_C1_326	56.2%	48%	76	33%	23.1
HWCTGDRXX_n01_C1_331	16.2%	49%	76	33%	0.1
HWCTGDRXX_n01_C1_332	52.5%	49%	76	33%	21.7
HWCTGDRXX_n01_C1_335	54.1%	49%	76	42%	23.9
HWCTGDRXX_n01_C1_346	49.7%	49%	76	25%	18.5
HWCTGDRXX_n01_C1_352	57.5%	50%	76	42%	15.2
HWCTGDRXX_n01_C1_365	53.2%	48%	76	33%	25.1
HWCTGDRXX_n01_C1_367	52.9%	49%	76	42%	25.3
HWCTGDRXX_n01_C1_37	53.0%	49%	76	42%	15.4
HWCTGDRXX_n01_C1_381	59.1%	49%	76	42%	22.5
HWCTGDRXX_n01_C1_384	52.4%	48%	76	33%	17.8
HWCTGDRXX_n01_C1_385	18.6%	50%	76	25%	0.2
HWCTGDRXX_n01_C1_386	61.0%	49%	76	42%	24.2
HWCTGDRXX_n01_C1_39	49.5%	48%	76	25%	18.3
HWCTGDRXX_n01_C1_392	57.4%	49%	76	42%	18.7
HWCTGDRXX_n01_C1_393	53.1%	49%	76	42%	21.2
HWCTGDRXX_n01_C1_396	54.2%	49%	76	33%	34.3
HWCTGDRXX_n01_C1_399	57.6%	48%	76	33%	36.0
HWCTGDRXX_n01_C1_402	48.4%	49%	76	25%	18.8
HWCTGDRXX_n01_C1_402_T2	58.0%	49%	76	42%	25.8
HWCTGDRXX_n01_C1_405	62.5%	49%	76	42%	26.8
HWCTGDRXX_n01_C1_405_T2	59.0%	50%	76	33%	18.9
HWCTGDRXX_n01_C1_411	56.1%	49%	76	42%	18.9
HWCTGDRXX_n01_C1_412	61.9%	49%	76	33%	46.1
HWCTGDRXX_n01_C1_47	49.8%	49%	76	25%	19.0
HWCTGDRXX_n01_C1_5	55.9%	48%	76	42%	24.3
HWCTGDRXX_n01_C1_51	61.0%	49%	76	42%	22.6
HWCTGDRXX_n01_C1_55	64.2%	49%	76	50%	26.7
HWCTGDRXX_n01_C1_58	54.6%	49%	76	42%	17.6
HWCTGDRXX_n01_C1_62	54.2%	49%	76	42%	13.6
HWCTGDRXX_n01_C1_64	61.7%	50%	76	50%	15.8
HWCTGDRXX_n01_C1_69	56.3%	49%	76	42%	18.2
HWCTGDRXX_n01_C1_70	57.2%	49%	76	50%	16.4
HWCTGDRXX_n01_C1_75	53.6%	49%	76	42%	23.4
HWCTGDRXX_n01_C1_77	52.3%	48%	76	42%	21.3
HWCTGDRXX_n01_C1_81	58.0%	50%	76	42%	19.3
HWCTGDRXX_n01_C1_85	51.3%	49%	76	42%	17.7
HWCTGDRXX_n01_C1_86	55.3%	49%	76	33%	18.5
HWCTGDRXX_n01_undetermined	59.5%	47%	76	50%	93.9

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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 ⁹⁵/₉₅ rows and ²/₂ columns.

Sample Name	Total Read Count	Portion (%)
undetermined_library	93,912,478	4.5
C1_1_	12,444,685	0.6
C1_5_	24,315,400	1.2
C1_11_	13,461,995	0.7
C1_14_	23,731,331	1.1
C1_22_	24,091,804	1.2
C1_37_	15,356,919	0.7
C1_39_	18,316,217	0.9
C1_47_	18,972,287	0.9
C1_51_	22,619,118	1.1
C1_55_	26,687,210	1.3
C1_58_	17,609,299	0.9
C1_62_	13,643,939	0.7
C1_64_	15,830,220	0.8
C1_69_	18,239,220	0.9
C1_70_	16,410,296	0.8
C1_75_	23,384,450	1.1
C1_77_	21,295,599	1.0
C1_81_	19,287,127	0.9
C1_85_	17,679,257	0.9
C1_86_	18,488,707	0.9
C1_100_	17,778,010	0.9
C1_108_	21,337,393	1.0
C1_118_	13,925,526	0.7
C1_124_	14,370,800	0.7
C1_125_	18,788,067	0.9
C1_126_	19,351,406	0.9
C1_135_	19,542,375	0.9
C1_139_	283,946	0.0
C1_146_	20,664,101	1.0
C1_148_	18,986,542	0.9
C1_149_	20,428,941	1.0
C1_155_	24,671,469	1.2
C1_162_	21,261,940	1.0
C1_169_	10,486,446	0.5
C1_170_	24,390,782	1.2
C1_177_	22,050,724	1.1
C1_185_	960,460	0.0
C1_208_	18,939,900	0.9
C1_209_	17,591,723	0.9
C1_213_	22,777,004	1.1
C1_215_	17,484,428	0.8
C1_220_	16,693,887	0.8
C1_221_	16,461,457	0.8
C1_225_	26,743,331	1.3
C1_227_	24,846,495	1.2
C1_246_	14,705,558	0.7
C1_253_	29,878,416	1.4
C1_262_	27,512,564	1.3
C1_264_	23,521,690	1.1
C1_269_	18,555,206	0.9
C1_270_	22,529,593	1.1
C1_275_	28,048,418	1.4
C1_278_	21,233,373	1.0
C1_279_	14,784,085	0.7
C1_280_	21,677,870	1.0
C1_281_	22,783,033	1.1
C1_286_	19,617,793	0.9
C1_287_	18,058,929	0.9
C1_290_	59,237,720	2.9
C1_296_	29,096,964	1.4
C1_297_	16,662,306	0.8
C1_298_	26,815,772	1.3
C1_302_	23,599,276	1.1
C1_304_	31,753,987	1.5
C1_311_	20,355,783	1.0
C1_313_	18,023,139	0.9
C1_314_	21,949,314	1.1
C1_317_	22,150,197	1.1
C1_318_	27,805,510	1.3
C1_319_	18,935,196	0.9
C1_321_	33,979,846	1.6
C1_324_	24,294,478	1.2
C1_326_	23,078,655	1.1
C1_331_	69,895	0.0
C1_332_	21,668,327	1.0
C1_335_	23,867,942	1.2
C1_346_	18,511,110	0.9
C1_352_	15,162,315	0.7
C1_365_	25,091,903	1.2
C1_367_	25,288,097	1.2
C1_381_	22,534,858	1.1
C1_384_	17,757,897	0.9
C1_385_	178,233	0.0
C1_386_	24,162,678	1.2
C1_392_	18,678,912	0.9
C1_393_	21,220,298	1.0
C1_396_	34,261,424	1.7
C1_399_	36,008,113	1.7
C1_402_	18,842,479	0.9
C1_405_	26,763,863	1.3
C1_411_	18,934,367	0.9
C1_412_	46,065,202	2.2
C1_402_T2_	25,843,535	1.2
C1_405_T2_	18,923,792	0.9

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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 (%)
GGGGGGGG	28895551.0	30.8
GAACCTCA	662192.0	0.7
GATCCTCA	466668.0	0.5
TGCGCATA	465006.0	0.5
CGGGGGGG	425355.0	0.5
CGGACAAA	424668.0	0.5
GGAACAAA	322569.0	0.3
GGGGGGGT	295471.0	0.3
CGTTAGGA	294866.0	0.3
CAACCTTA	281541.0	0.3
CGTTAAGA	276996.0	0.3
CACCGATA	261088.0	0.3
ACAGTGAA	256841.0	0.3
CAATTGGA	256461.0	0.3
GTGTGAGA	255680.0	0.3
AGTCATCA	255212.0	0.3
CACGCTAA	253053.0	0.3
CACACTTA	249221.0	0.3
ACACCTTA	241450.0	0.3
AACCGATA	236701.0	0.2

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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
2.0	2,553,348,096	2,067,074,622	4.5	0.4

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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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Barcodes of Undetermined Reads

Run 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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Barcodes of Undetermined Reads

Table Gebk: Columns

Run Statistics

Table Ygwc: 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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