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If you use plots from MultiQC in a publication or presentation, please cite:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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About MultiQC

This report was generated using MultiQC, version 1.10.dev0

You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

MultiQC is published in Bioinformatics:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

HTSMultiQC-cleaning-report

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

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Report generated on 2021-12-09, 11:53 based on data in: /share/workshop/meta_workshop/jli/meta_example/01-HTS_Preproc/mRNA

HTStream

HTStream quality control and processing pipeline for High Throughput Sequencing data.

Processing Overview

General statistics from the HTStream pipeline.

Preprocessing Statistics

Fragment Reduction

Provides scaled statistics collected throughout the preprocessing pipeline, highlighting variable statistics across experiment.

Basepair Reduction

Provides scaled statistics collected throughout the preprocessing pipeline, highlighting variable statistics across experiment.

hts_Stats

Generates a JSON formatted file containing a set of statistical measures about the input read data.

Showing ⁴⁸/₄₈ rows and ⁶/₆ columns.

Sample Name	% PE	% R1 Q30	% R2 Q30	GC Content	N Content
ANG_301	100.00%	90.12%	88.44%	48.47%	0.0126%
ANG_302	100.00%	91.88%	92.84%	45.65%	0.0135%
ANG_303	100.00%	93.45%	92.98%	45.34%	0.0115%
ANG_304	100.00%	94.29%	92.62%	47.45%	0.0176%
ANG_305	100.00%	93.83%	92.39%	48.05%	0.0114%
ANG_307	100.00%	94.31%	91.16%	51.97%	0.0114%
ANG_308	100.00%	93.84%	93.03%	48.85%	0.0113%
ANG_401	100.00%	93.83%	94.12%	44.96%	0.0197%
ANG_402	100.00%	91.78%	92.16%	49.94%	0.0194%
ANG_403	100.00%	93.49%	90.14%	50.90%	0.0193%
ANG_404	100.00%	94.26%	93.84%	45.91%	0.0178%
ANG_407	100.00%	94.46%	93.96%	42.19%	0.0223%
ANG_501	100.00%	93.66%	91.47%	49.03%	0.0196%
ANG_503	100.00%	90.66%	89.86%	45.48%	0.0131%
ANG_505	100.00%	94.09%	90.47%	50.84%	0.0226%
ANG_506	100.00%	93.58%	91.93%	49.62%	0.0198%
CHAR_601	100.00%	94.45%	93.74%	42.88%	0.0202%
CHAR_604	100.00%	90.80%	90.10%	43.55%	0.0132%
CHAR_608	100.00%	90.45%	89.25%	43.78%	0.0129%
CHAR_611	100.00%	94.29%	93.06%	44.46%	0.0197%
CHAR_612	100.00%	93.94%	93.69%	46.83%	0.0176%
CHAR_701	100.00%	94.21%	93.62%	44.49%	0.0201%
CHAR_702	100.00%	92.36%	89.66%	46.29%	0.0197%
CHAR_703	100.00%	89.68%	86.89%	51.81%	0.0125%
CHAR_704	100.00%	93.00%	88.86%	51.62%	0.0214%
CHAR_705	100.00%	92.03%	91.16%	48.55%	0.0194%
CHAR_706	100.00%	93.98%	93.89%	44.32%	0.0199%
CHAR_707	100.00%	94.19%	92.12%	51.68%	0.0196%
CHAR_708	100.00%	94.13%	91.78%	52.93%	0.0176%
CHAR_709	100.00%	95.68%	93.15%	45.55%	0.0231%
CHAR_710	100.00%	94.22%	92.43%	47.69%	0.0219%
CHAR_712	100.00%	94.38%	92.81%	48.30%	0.0225%
HYB_101	100.00%	89.10%	87.14%	51.88%	0.0127%
HYB_103	100.00%	91.11%	86.91%	53.18%	0.0129%
HYB_104	100.00%	93.90%	93.01%	47.03%	0.0196%
HYB_105	100.00%	93.72%	93.98%	44.29%	0.0196%
HYB_106	100.00%	93.78%	92.68%	47.35%	0.0113%
HYB_107	100.00%	93.41%	93.16%	46.03%	0.0114%
HYB_112	100.00%	93.23%	91.71%	50.03%	0.0114%
HYB_201	100.00%	94.44%	91.48%	51.52%	0.0230%
HYB_202	100.00%	94.56%	93.84%	44.52%	0.0198%
HYB_203	100.00%	94.01%	92.93%	47.64%	0.0201%
HYB_205	100.00%	93.66%	92.97%	43.59%	0.0176%
HYB_206	100.00%	95.40%	93.26%	46.08%	0.0232%
HYB_207	100.00%	90.17%	90.55%	42.45%	0.0130%
HYB_208	100.00%	94.31%	93.57%	45.26%	0.0176%
HYB_209	100.00%	94.08%	93.14%	43.20%	0.0178%
HYB_210	100.00%	92.79%	93.01%	44.53%	0.0176%

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

Sort	Group	Column	Description	ID	Scale
\|\|	% PE	% PE	percentage of paried end reads	`St_PE_Fraction1`	None
\|\|	% R1 Q30	% R1 Q30	percentage of read 1 bps Q30 or greater	`St_R1_Q301`	None
\|\|	% R2 Q30	% R2 Q30	percentage of read 2 bps Q30 or greater	`St_R2_Q301`	None
\|\|	GC Content	GC Content	Percentage of bps that are G or C	`St_GC_Content1`	None
\|\|	N Content	N Content	Percentage of bps that are N	`St_N_Content1`	None
\|\|	Notes	Notes	Notes	`St_Notes1`	None

Read Lengths: Paired End

Distribution of read lengths for each sample.

Notice: Each sample has a uniform read length distribution.

Showing ⁴⁸/₄₈ rows and ²/₂ columns.

Sample Name	R1 Read Lengths	R2 Read Lengths
ANG_301	125	125
ANG_302	125	125
ANG_303	125	125
ANG_304	125	125
ANG_305	125	125
ANG_307	125	125
ANG_308	125	125
ANG_401	125	125
ANG_402	125	125
ANG_403	125	125
ANG_404	125	125
ANG_407	125	125
ANG_501	125	125
ANG_503	125	125
ANG_505	125	125
ANG_506	125	125
CHAR_601	125	125
CHAR_604	125	125
CHAR_608	125	125
CHAR_611	125	125
CHAR_612	125	125
CHAR_701	125	125
CHAR_702	125	125
CHAR_703	125	125
CHAR_704	125	125
CHAR_705	125	125
CHAR_706	125	125
CHAR_707	125	125
CHAR_708	125	125
CHAR_709	125	125
CHAR_710	125	125
CHAR_712	125	125
HYB_101	125	125
HYB_103	125	125
HYB_104	125	125
HYB_105	125	125
HYB_106	125	125
HYB_107	125	125
HYB_112	125	125
HYB_201	125	125
HYB_202	125	125
HYB_203	125	125
HYB_205	125	125
HYB_206	125	125
HYB_207	125	125
HYB_208	125	125
HYB_209	125	125
HYB_210	125	125

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|		R1 Read Lengths	R1 Read Lengths	Length of R1 reads (uniform for each sample).	`St_Read_Lengths_R1_4725205363762`	None
\|\|		R2 Read Lengths	R2 Read Lengths	Length of R2 reads (uniform for each sample).	`St_Read_Lengths_R2_4725205363762`	None

Base by Cycle: Paired End

Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.

Quality by Cycle: Paired End

Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

hts_SeqScreener

A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.

Showing ⁴⁸/₄₈ rows and ³/₃ columns.

Sample Name	PE hits	% PE Hits
ANG_301	3681	0.1104%
ANG_302	1367	0.1190%
ANG_303	2990	0.0907%
ANG_304	2162	0.0797%
ANG_305	4600	0.1345%
ANG_307	2128	0.0829%
ANG_308	4874	0.1512%
ANG_401	3991	0.1304%
ANG_402	4745	0.2002%
ANG_403	2968	0.1628%
ANG_404	5134	0.1753%
ANG_407	10516	0.3281%
ANG_501	4295	0.1633%
ANG_503	4133	0.1168%
ANG_505	11432	0.5591%
ANG_506	4999	0.1918%
CHAR_601	4737	0.1207%
CHAR_604	7854	0.1608%
CHAR_608	4048	0.0833%
CHAR_611	2695	0.0855%
CHAR_612	4940	0.1763%
CHAR_701	3923	0.1269%
CHAR_702	3164	0.1819%
CHAR_703	5156	0.1969%
CHAR_704	4153	0.2424%
CHAR_705	2256	0.1204%
CHAR_706	3315	0.0818%
CHAR_707	1994	0.0604%
CHAR_708	2822	0.1226%
CHAR_709	5255	0.1617%
CHAR_710	8017	0.2962%
CHAR_712	6727	0.2252%
HYB_101	7656	0.2346%
HYB_103	3426	0.1194%
HYB_104	4649	0.1420%
HYB_105	4645	0.1279%
HYB_106	4475	0.1375%
HYB_107	4420	0.1261%
HYB_112	3819	0.1652%
HYB_201	4745	0.2018%
HYB_202	4037	0.0915%
HYB_203	4359	0.1728%
HYB_205	2789	0.1005%
HYB_206	4317	0.1561%
HYB_207	6967	0.1514%
HYB_208	2640	0.0772%
HYB_209	3565	0.1105%
HYB_210	3992	0.1272%

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

Sort	Group	Column	Description	ID	Scale
\|\|	PE hits	PE hits	Number of Paired End Reads with Sequence	`Ss_PE_hits1`	None
\|\|	% PE Lost	% PE Hits	Percentage of Paired End Reads Lost	`Ss_PE_%_hits1`	None
\|\|	Notes	Notes	Notes	`Ss_Notes1`	None

hts_AdapterTrimmer

Trims adapters which are sequenced when the fragment insert length is shorter than the read length.

Showing ⁴⁸/₄₈ rows and ⁴/₄ columns.

Sample Name	% Bp Lost	% Adapters	Avg. Bps Trimmed
ANG_301	1.99%	37.39%	13.33
ANG_302	0.84%	11.01%	19.05
ANG_303	2.15%	36.94%	14.57
ANG_304	1.78%	31.28%	14.20
ANG_305	1.93%	35.26%	13.68
ANG_307	1.70%	33.12%	12.86
ANG_308	1.66%	31.46%	13.18
ANG_401	2.06%	38.92%	13.22
ANG_402	1.97%	35.13%	14.05
ANG_403	2.08%	31.32%	16.61
ANG_404	2.40%	41.77%	14.37
ANG_407	2.07%	35.14%	14.73
ANG_501	1.63%	26.44%	15.45
ANG_503	2.34%	39.84%	14.68
ANG_505	1.70%	24.59%	17.30
ANG_506	1.65%	27.89%	14.82
CHAR_601	2.79%	48.60%	14.35
CHAR_604	2.49%	44.27%	14.07
CHAR_608	2.51%	42.96%	14.63
CHAR_611	1.85%	31.03%	14.92
CHAR_612	2.43%	42.53%	14.30
CHAR_701	2.56%	43.63%	14.66
CHAR_702	1.86%	28.44%	16.35
CHAR_703	2.08%	35.59%	14.64
CHAR_704	2.38%	31.63%	18.81
CHAR_705	1.86%	28.13%	16.50
CHAR_706	2.36%	41.35%	14.25
CHAR_707	1.63%	30.11%	13.54
CHAR_708	1.49%	27.67%	13.48
CHAR_709	1.85%	35.21%	13.10
CHAR_710	1.87%	31.88%	14.65
CHAR_712	1.88%	33.47%	14.04
HYB_101	1.95%	33.33%	14.64
HYB_103	2.24%	36.75%	15.26
HYB_104	2.36%	38.82%	15.18
HYB_105	2.41%	44.35%	13.58
HYB_106	2.31%	39.77%	14.55
HYB_107	2.13%	38.56%	13.83
HYB_112	2.20%	39.92%	13.78
HYB_201	1.55%	27.22%	14.23
HYB_202	2.44%	42.42%	14.40
HYB_203	1.95%	33.04%	14.75
HYB_205	1.75%	29.88%	14.65
HYB_206	2.09%	35.66%	14.64
HYB_207	2.18%	39.86%	13.65
HYB_208	1.85%	33.98%	13.63
HYB_209	2.69%	45.53%	14.75
HYB_210	2.38%	40.53%	14.68

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

Sort	Group	Column	Description	ID	Scale
\|\|	% Bp Lost	% Bp Lost	Percentage of Input bps (SE and PE) trimmed.	`At_%_BP_Lost1`	None
\|\|	% Adapters	% Adapters	Percentage of Reads (SE and PE) with an Adapter	`At_%_Adapters1`	None
\|\|	Avg. Bps Trimmed	Avg. Bps Trimmed	Average Number of basepairs trimmed from reads	`At_Avg_BP_Trimmed1`	None
\|\|	Notes	Notes	Notes	`At_Notes1`	None

AdapterTrimmer: Trimmed Basepairs Composition

Composition of basepairs trimmed from the ends of paired end and single end reads.

hts_Overlapper

Attempts to overlap paired end reads to produce the original fragment, trims adapters, and can correct sequencing errors.

Showing ⁴⁸/₄₈ rows and ²/₂ columns.

Sample Name	% Overlapped	Notes
ANG_301	94.30%
ANG_302	26.09%
ANG_303	91.95%
ANG_304	89.28%
ANG_305	91.57%
ANG_307	91.05%
ANG_308	91.46%
ANG_401	93.55%
ANG_402	92.20%
ANG_403	84.39%
ANG_404	94.32%
ANG_407	91.16%
ANG_501	85.60%
ANG_503	94.10%
ANG_505	80.28%
ANG_506	86.93%
CHAR_601	94.69%
CHAR_604	93.81%
CHAR_608	93.56%
CHAR_611	86.42%
CHAR_612	94.54%
CHAR_701	94.88%
CHAR_702	83.48%
CHAR_703	92.01%
CHAR_704	79.25%
CHAR_705	85.85%
CHAR_706	94.04%
CHAR_707	90.01%
CHAR_708	91.15%
CHAR_709	93.27%
CHAR_710	89.10%
CHAR_712	91.21%
HYB_101	88.42%
HYB_103	88.68%
HYB_104	89.94%
HYB_105	93.61%
HYB_106	90.13%
HYB_107	93.50%
HYB_112	90.41%
HYB_201	85.05%
HYB_202	93.63%
HYB_203	90.35%
HYB_205	87.30%
HYB_206	92.07%
HYB_207	92.14%
HYB_208	91.68%
HYB_209	91.04%
HYB_210	92.92%

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
\|\|		% Overlapped	% Overlapped	Percentage of Reads with Overlap.	`Ov_%_Overlapped1`	None
\|\|		Notes	Notes	Notes	`Ov_Notes1`	None

Overlapper: Overlap Composition

Plots the quantities of insert types for each sample.

Overlapper: Overlapped Lengths

Plots the lengths of paired end read overlaps.

hts_QWindowTrim

Uses a sliding window approach to remove the low quality ends of reads.

Showing ⁴⁸/₄₈ rows and ⁶/₆ columns.

Sample Name	% Bp Lost	% R1 of Bp Lost	% R2 of Bp Lost	% SE of Bp Lost	Avg. Bps Trimmed
ANG_301	0.74%	27.05%	61.19%	11.76%	1.17
ANG_302	1.73%	45.45%	53.97%	0.58%	3.87
ANG_303	0.59%	29.34%	63.36%	7.30%	0.96
ANG_304	0.63%	26.72%	65.83%	7.45%	1.06
ANG_305	0.61%	26.45%	65.43%	8.12%	0.99
ANG_307	0.82%	21.61%	70.43%	7.96%	1.33
ANG_308	0.58%	26.95%	65.38%	7.67%	0.95
ANG_401	0.43%	32.02%	59.15%	8.84%	0.67
ANG_402	0.70%	32.27%	60.52%	7.21%	1.14
ANG_403	1.76%	21.89%	75.18%	2.93%	3.02
ANG_404	0.41%	28.42%	61.99%	9.59%	0.64
ANG_407	0.53%	30.56%	63.09%	6.35%	0.88
ANG_501	1.34%	23.85%	72.54%	3.61%	2.30
ANG_503	0.66%	29.84%	59.04%	11.13%	1.05
ANG_505	1.69%	23.31%	74.50%	2.19%	3.03
ANG_506	1.23%	25.40%	70.86%	3.73%	2.10
CHAR_601	0.40%	28.28%	60.65%	11.06%	0.61
CHAR_604	0.67%	30.53%	59.20%	10.27%	1.05
CHAR_608	0.72%	29.71%	59.41%	10.88%	1.13
CHAR_611	0.76%	27.62%	66.61%	5.77%	1.31
CHAR_612	0.43%	28.80%	61.72%	9.48%	0.68
CHAR_701	0.39%	27.60%	60.76%	11.64%	0.61
CHAR_702	3.50%	33.50%	65.18%	1.32%	5.97
CHAR_703	1.07%	24.63%	66.18%	9.19%	1.74
CHAR_704	2.57%	24.59%	73.99%	1.43%	4.50
CHAR_705	1.64%	27.86%	69.37%	2.77%	2.78
CHAR_706	0.48%	31.74%	59.18%	9.08%	0.76
CHAR_707	0.69%	24.76%	67.04%	8.21%	1.15
CHAR_708	0.65%	24.09%	66.71%	9.19%	1.09
CHAR_709	0.54%	22.23%	68.82%	8.95%	0.87
CHAR_710	1.16%	25.47%	71.31%	3.22%	1.91
CHAR_712	0.86%	25.60%	70.07%	4.32%	1.39
HYB_101	1.20%	29.43%	63.05%	7.52%	2.02
HYB_103	1.13%	23.77%	67.73%	8.50%	1.88
HYB_104	0.58%	29.66%	62.88%	7.46%	0.96
HYB_105	0.45%	32.01%	58.96%	9.04%	0.70
HYB_106	0.62%	29.47%	63.37%	7.17%	1.03
HYB_107	0.46%	30.54%	59.92%	9.54%	0.73
HYB_112	1.35%	35.99%	60.59%	3.41%	2.19
HYB_201	1.18%	23.40%	73.32%	3.28%	2.04
HYB_202	0.42%	29.39%	59.49%	11.12%	0.66
HYB_203	0.63%	27.75%	64.85%	7.40%	1.05
HYB_205	0.68%	31.15%	62.87%	5.97%	1.16
HYB_206	0.54%	23.90%	68.22%	7.89%	0.88
HYB_207	0.73%	35.07%	56.47%	8.46%	1.17
HYB_208	0.48%	29.10%	62.17%	8.72%	0.79
HYB_209	0.80%	26.27%	68.82%	4.92%	1.28
HYB_210	0.63%	34.00%	58.96%	7.04%	1.01

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

Sort	Group	Column	Description	ID	Scale
\|\|	% Bp Lost	% Bp Lost	Percentage of Input bps (SE and PE) trimmed.	`Qt_%_BP_Lost1`	None
\|\|	% Bp Lost from R1	% R1 of Bp Lost	Percentage of total trimmed bps.	`Qt_%_R1_BP_Lost1`	None
\|\|	% Bp Lost from R2	% R2 of Bp Lost	Percentage of total trimmed bps.	`Qt_%_R2_BP_Lost1`	None
\|\|	% Bp Lost from SE	% SE of Bp Lost	Percentage of total trimmed bps.	`Qt_%_SE_BP_Lost1`	None
\|\|	Avg. Bpss Trimmed	Avg. Bps Trimmed	Average Number of Basepairs Trimmed per Read	`Qt_Avg_BP_Trimmed1`	None
\|\|	Notes	Notes	Notes	`Qt_Notes1`	None

QWindowTrim: Trimmed Basepairs Composition

Plots the number of low quality basepairs trimmed from ends of paired end and single end reads.

hts_LengthFilter

Discards reads below a minimum length threshold.

Showing ⁴⁸/₄₈ rows and ⁴/₄ columns.

Sample Name	% PE Lost	% PE Orphaned	% SE Lost
ANG_301	5.93%	5.43%	0.03%
ANG_302	0.63%	0.60%	0.47%
ANG_303	2.98%	2.74%	0.06%
ANG_304	2.47%	2.31%	0.05%
ANG_305	3.17%	2.96%	0.03%
ANG_307	4.29%	4.05%	0.06%
ANG_308	3.22%	3.05%	0.03%
ANG_401	2.65%	2.43%	0.03%
ANG_402	3.60%	3.32%	0.07%
ANG_403	6.58%	6.07%	0.34%
ANG_404	3.04%	2.86%	0.02%
ANG_407	2.32%	2.22%	0.02%
ANG_501	5.01%	4.46%	0.30%
ANG_503	4.75%	4.33%	0.02%
ANG_505	4.08%	3.70%	0.35%
ANG_506	5.10%	4.47%	0.29%
CHAR_601	3.23%	3.02%	0.03%
CHAR_604	4.68%	4.25%	0.04%
CHAR_608	4.71%	4.35%	0.04%
CHAR_611	2.57%	2.34%	0.13%
CHAR_612	3.36%	3.09%	0.04%
CHAR_701	3.30%	3.07%	0.02%
CHAR_702	9.24%	8.28%	0.55%
CHAR_703	6.86%	6.36%	0.04%
CHAR_704	6.18%	5.60%	0.58%
CHAR_705	6.16%	5.32%	0.52%
CHAR_706	3.26%	2.99%	0.02%
CHAR_707	3.06%	2.80%	0.09%
CHAR_708	3.28%	3.11%	0.04%
CHAR_709	3.65%	3.47%	0.05%
CHAR_710	4.98%	4.47%	0.27%
CHAR_712	4.17%	3.73%	0.18%
HYB_101	4.21%	3.85%	0.05%
HYB_103	4.35%	4.05%	0.05%
HYB_104	2.23%	2.08%	0.04%
HYB_105	2.95%	2.75%	0.03%
HYB_106	2.48%	2.32%	0.05%
HYB_107	2.85%	2.66%	0.06%
HYB_112	4.67%	4.19%	0.04%
HYB_201	3.43%	3.16%	0.17%
HYB_202	2.54%	2.31%	0.02%
HYB_203	2.88%	2.67%	0.06%
HYB_205	2.07%	1.94%	0.05%
HYB_206	2.85%	2.69%	0.04%
HYB_207	3.70%	3.34%	0.03%
HYB_208	2.26%	2.13%	0.03%
HYB_209	4.36%	4.03%	0.10%
HYB_210	3.47%	3.26%	0.03%

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Sort	Group	Column	Description	ID	Scale
\|\|	% PE Lost	% PE Lost	Percentage of Paired End Reads Lost	`Lf_PE_loss1`	None
\|\|	% PE Orphaned	% PE Orphaned	Percentage of Paired End Reads Orphaned (Now Single End)	`Lf_PE_Orphaned1`	None
\|\|	% SE Lost	% SE Lost	Percentage of Single End Reads Lost	`Lf_SE_loss1`	None
\|\|	Notes	Notes	Notes	`Lf_Notes1`	None

hts_Stats 2

Generates a JSON formatted file containing a set of statistical measures about the input read data.

Showing ⁴⁸/₄₈ rows and ⁸/₈ columns.

Sample Name	% PE	% SE	% R1 Q30	% R2 Q30	% SE Q30	GC Content	N Content
ANG_301	5.37%	94.63%	89.35%	85.90%	96.88%	48.56%	0.0117%
ANG_302	73.55%	26.45%	93.06%	94.11%	97.96%	45.70%	0.0110%
ANG_303	7.82%	92.18%	92.57%	89.98%	98.08%	45.60%	0.0093%
ANG_304	10.46%	89.54%	93.92%	90.74%	97.93%	47.49%	0.0163%
ANG_305	8.16%	91.84%	93.03%	89.57%	97.99%	48.31%	0.0093%
ANG_307	8.57%	91.43%	93.41%	87.61%	97.84%	52.23%	0.0094%
ANG_308	8.27%	91.73%	93.05%	90.60%	98.02%	49.02%	0.0094%
ANG_401	6.28%	93.72%	92.83%	91.51%	98.37%	45.12%	0.0173%
ANG_402	7.53%	92.47%	91.02%	88.32%	97.83%	50.21%	0.0175%
ANG_403	14.64%	85.36%	92.20%	84.95%	97.65%	51.32%	0.0170%
ANG_404	5.51%	94.49%	93.31%	91.00%	98.39%	46.11%	0.0158%
ANG_407	8.64%	91.36%	93.69%	92.42%	98.46%	42.24%	0.0079%
ANG_501	13.72%	86.28%	92.37%	86.37%	97.80%	49.55%	0.0171%
ANG_503	5.63%	94.37%	89.75%	87.33%	97.19%	45.61%	0.0117%
ANG_505	18.99%	81.01%	93.06%	87.63%	97.85%	51.17%	0.0082%
ANG_506	12.45%	87.55%	92.27%	87.03%	97.87%	50.10%	0.0172%
CHAR_601	5.14%	94.86%	93.56%	91.33%	98.52%	42.94%	0.0171%
CHAR_604	5.90%	94.10%	89.83%	87.56%	97.44%	43.61%	0.0116%
CHAR_608	6.14%	93.86%	89.42%	86.72%	97.22%	43.84%	0.0114%
CHAR_611	13.25%	86.75%	93.65%	90.43%	98.00%	44.62%	0.0170%
CHAR_612	5.28%	94.72%	92.94%	90.71%	98.34%	47.03%	0.0156%
CHAR_701	4.95%	95.05%	93.41%	91.11%	98.34%	44.60%	0.0174%
CHAR_702	15.08%	84.92%	91.08%	83.84%	97.82%	47.04%	0.0174%
CHAR_703	7.45%	92.55%	89.10%	84.41%	96.46%	51.96%	0.0114%
CHAR_704	19.58%	80.42%	91.47%	84.68%	97.77%	52.22%	0.0076%
CHAR_705	13.35%	86.65%	90.88%	85.38%	97.77%	49.15%	0.0170%
CHAR_706	5.77%	94.23%	93.20%	91.49%	98.31%	44.45%	0.0166%
CHAR_707	9.70%	90.30%	93.40%	88.95%	97.82%	51.85%	0.0171%
CHAR_708	8.56%	91.44%	93.57%	89.37%	97.77%	53.10%	0.0164%
CHAR_709	6.49%	93.51%	94.87%	90.84%	98.46%	45.79%	0.0084%
CHAR_710	10.39%	89.61%	92.45%	87.75%	98.34%	48.23%	0.0079%
CHAR_712	8.44%	91.56%	92.51%	88.50%	98.40%	48.76%	0.0079%
HYB_101	11.10%	88.90%	88.97%	84.76%	96.28%	52.03%	0.0115%
HYB_103	10.84%	89.16%	90.70%	84.88%	96.45%	53.23%	0.0114%
HYB_104	9.85%	90.15%	93.11%	90.47%	98.04%	47.16%	0.0171%
HYB_105	6.20%	93.80%	92.73%	91.35%	98.39%	44.38%	0.0169%
HYB_106	9.63%	90.37%	93.09%	90.36%	97.97%	47.43%	0.0091%
HYB_107	6.32%	93.68%	92.43%	90.78%	98.13%	46.18%	0.0092%
HYB_112	9.15%	90.85%	92.22%	88.06%	97.99%	50.24%	0.0091%
HYB_201	14.47%	85.53%	93.25%	88.52%	98.03%	51.84%	0.0082%
HYB_202	6.21%	93.79%	93.83%	91.41%	98.34%	44.65%	0.0164%
HYB_203	9.38%	90.62%	93.16%	90.17%	98.02%	47.85%	0.0178%
HYB_205	12.44%	87.56%	93.07%	91.03%	97.96%	43.65%	0.0161%
HYB_206	7.71%	92.29%	94.60%	91.33%	98.41%	46.28%	0.0085%
HYB_207	7.57%	92.43%	89.32%	88.38%	97.31%	42.43%	0.0117%
HYB_208	8.13%	91.87%	93.64%	91.36%	98.22%	45.41%	0.0163%
HYB_209	8.58%	91.42%	92.95%	89.22%	98.38%	43.37%	0.0154%
HYB_210	6.84%	93.16%	92.16%	90.50%	98.18%	44.66%	0.0157%

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Sort	Group	Column	Description	ID	Scale
\|\|	% PE	% PE	percentage of paried end reads	`St_PE_Fraction2`	None
\|\|	% SE	% SE	percentage of paried end reads	`St_SE_Fraction2`	None
\|\|	% R1 Q30	% R1 Q30	percentage of read 1 bps Q30 or greater	`St_R1_Q302`	None
\|\|	% R2 Q30	% R2 Q30	percentage of read 2 bps Q30 or greater	`St_R2_Q302`	None
\|\|	% SE Q30	% SE Q30	percentage of single end read bps Q30 or greater	`St_SE_Q302`	None
\|\|	GC Content	GC Content	Percentage of bps that are G or C	`St_GC_Content2`	None
\|\|	N Content	N Content	Percentage of bps that are N	`St_N_Content2`	None
\|\|	Notes	Notes	Notes	`St_Notes2`	None

Read Lengths: Paired End

Distribution of read lengths for each sample.

Base by Cycle: Paired End

Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.

Quality by Cycle: Paired End

Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

Read Lengths: Single End

Distribution of read lengths for each sample.

Base by Cycle: Single End

Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.

Quality by Cycle: Single End

Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

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HTSMultiQC-cleaning-report

HTStream

Processing Overview

Preprocessing Statistics

Fragment Reduction

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hts_Stats

Table Vqcs: Columns

Read Lengths: Paired End

Table Nxgi: Columns

Base by Cycle: Paired End

Quality by Cycle: Paired End

hts_SeqScreener

Table Nrzm: Columns

hts_AdapterTrimmer

Table Inbe: Columns

AdapterTrimmer: Trimmed Basepairs Composition

hts_Overlapper

Table Ixgm: Columns

Overlapper: Overlap Composition

Overlapper: Overlapped Lengths

hts_QWindowTrim

Table Anvo: Columns

QWindowTrim: Trimmed Basepairs Composition

hts_LengthFilter

Table Qkdr: Columns

hts_Stats 2

Table Fnph: Columns

Read Lengths: Paired End

Base by Cycle: Paired End

Quality by Cycle: Paired End

Read Lengths: Single End

Base by Cycle: Single End

Quality by Cycle: Single End

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