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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, 11:49 based on data in: /share/workshop/meta_workshop/jli/meta_example/01-HTS_Preproc/DNA

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%	94.56%	90.11%	45.49%	0.0183%
ANG_302	100.00%	94.02%	89.12%	47.42%	0.0183%
ANG_303	100.00%	88.96%	83.42%	47.77%	0.0321%
ANG_304	100.00%	89.80%	84.41%	46.62%	0.0323%
ANG_305	100.00%	89.67%	84.32%	46.99%	0.0319%
ANG_307	100.00%	89.18%	82.93%	47.48%	0.0303%
ANG_308	100.00%	89.64%	83.30%	47.23%	0.0320%
ANG_401	100.00%	89.22%	80.82%	47.35%	0.0330%
ANG_402	100.00%	88.94%	78.81%	48.32%	0.0322%
ANG_403	100.00%	89.51%	83.47%	48.14%	0.0326%
ANG_404	100.00%	88.70%	78.46%	48.62%	0.0324%
ANG_407	100.00%	88.83%	80.25%	49.35%	0.0332%
ANG_501	100.00%	89.58%	80.58%	46.56%	0.0324%
ANG_503	100.00%	89.42%	79.49%	46.65%	0.0326%
ANG_505	100.00%	93.43%	87.40%	46.37%	0.0520%
ANG_506	100.00%	92.67%	82.22%	47.26%	0.0495%
CHAR_601	100.00%	93.87%	86.64%	41.33%	0.0516%
CHAR_604	100.00%	93.78%	86.33%	42.73%	0.0524%
CHAR_608	100.00%	92.70%	78.72%	45.21%	0.0474%
CHAR_611	100.00%	92.57%	80.91%	47.30%	0.0490%
CHAR_612	100.00%	91.85%	80.27%	46.74%	0.0344%
CHAR_701	100.00%	91.49%	77.35%	47.37%	0.0322%
CHAR_702	100.00%	92.51%	81.76%	43.31%	0.0348%
CHAR_703	100.00%	92.01%	81.77%	47.20%	0.0337%
CHAR_704	100.00%	92.09%	84.11%	48.06%	0.0334%
CHAR_705	100.00%	92.20%	86.57%	48.07%	0.0341%
CHAR_706	100.00%	93.39%	80.99%	47.50%	0.0278%
CHAR_707	100.00%	94.08%	90.71%	47.26%	0.0286%
CHAR_708	100.00%	93.97%	90.51%	47.14%	0.0272%
CHAR_709	100.00%	93.59%	83.32%	45.47%	0.0278%
CHAR_710	100.00%	93.48%	88.76%	48.57%	0.0283%
CHAR_712	100.00%	93.53%	88.81%	47.02%	0.0279%
HYB_101	100.00%	92.28%	86.93%	47.40%	0.0259%
HYB_103	100.00%	92.13%	86.47%	47.73%	0.0263%
HYB_104	100.00%	92.14%	87.30%	47.26%	0.0269%
HYB_105	100.00%	92.49%	83.99%	47.47%	0.0260%
HYB_106	100.00%	92.54%	82.63%	47.79%	0.0265%
HYB_107	100.00%	92.63%	87.50%	46.04%	0.0256%
HYB_112	100.00%	94.94%	88.15%	47.14%	0.0112%
HYB_201	100.00%	94.83%	86.35%	47.41%	0.0107%
HYB_202	100.00%	94.86%	85.63%	45.99%	0.0104%
HYB_203	100.00%	94.70%	89.94%	47.20%	0.0105%
HYB_205	100.00%	94.83%	90.41%	46.71%	0.0108%
HYB_206	100.00%	94.72%	90.17%	46.55%	0.0106%
HYB_207	100.00%	94.09%	89.49%	47.58%	0.0180%
HYB_208	100.00%	93.93%	85.58%	48.92%	0.0184%
HYB_209	100.00%	94.24%	86.95%	48.35%	0.0182%
HYB_210	100.00%	93.73%	85.50%	49.16%	0.0186%

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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	100	100
ANG_302	100	100
ANG_303	100	100
ANG_304	100	100
ANG_305	100	100
ANG_307	100	100
ANG_308	100	100
ANG_401	100	100
ANG_402	100	100
ANG_403	100	100
ANG_404	100	100
ANG_407	100	100
ANG_501	100	100
ANG_503	100	100
ANG_505	100	100
ANG_506	100	100
CHAR_601	100	100
CHAR_604	100	100
CHAR_608	100	100
CHAR_611	100	100
CHAR_612	100	100
CHAR_701	100	100
CHAR_702	100	100
CHAR_703	100	100
CHAR_704	100	100
CHAR_705	100	100
CHAR_706	100	100
CHAR_707	100	100
CHAR_708	100	100
CHAR_709	100	100
CHAR_710	100	100
CHAR_712	100	100
HYB_101	100	100
HYB_103	100	100
HYB_104	100	100
HYB_105	100	100
HYB_106	100	100
HYB_107	100	100
HYB_112	100	100
HYB_201	100	100
HYB_202	100	100
HYB_203	100	100
HYB_205	100	100
HYB_206	100	100
HYB_207	100	100
HYB_208	100	100
HYB_209	100	100
HYB_210	100	100

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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_53230591364572`	None
\|\|		R2 Read Lengths	R2 Read Lengths	Length of R2 reads (uniform for each sample).	`St_Read_Lengths_R2_53230591364572`	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	8720	0.2353%
ANG_302	7856	0.2358%
ANG_303	13385	0.4684%
ANG_304	14049	0.4006%
ANG_305	10536	0.3499%
ANG_307	14630	0.4339%
ANG_308	14639	0.4204%
ANG_401	12088	0.4155%
ANG_402	18678	0.6065%
ANG_403	19551	0.6489%
ANG_404	22584	0.6161%
ANG_407	19240	0.5754%
ANG_501	15930	0.5621%
ANG_503	24834	0.7798%
ANG_505	8982	0.2795%
ANG_506	15971	0.5735%
CHAR_601	6313	0.2754%
CHAR_604	8263	0.2572%
CHAR_608	7403	0.2914%
CHAR_611	6875	0.2264%
CHAR_612	4291	0.1972%
CHAR_701	6725	0.2374%
CHAR_702	7136	0.2325%
CHAR_703	7497	0.2402%
CHAR_704	7794	0.1973%
CHAR_705	7925	0.2246%
CHAR_706	7855	0.4032%
CHAR_707	12104	0.3361%
CHAR_708	9570	0.2808%
CHAR_709	12331	0.5264%
CHAR_710	11343	0.3253%
CHAR_712	15083	0.6870%
HYB_101	6883	0.1662%
HYB_103	5878	0.1483%
HYB_104	5604	0.1608%
HYB_105	7059	0.1756%
HYB_106	5963	0.1800%
HYB_107	8317	0.1969%
HYB_112	6747	0.2125%
HYB_201	5636	0.2009%
HYB_202	5969	0.2058%
HYB_203	6403	0.1871%
HYB_205	5922	0.2248%
HYB_206	5664	0.1588%
HYB_207	7224	0.2359%
HYB_208	6829	0.2291%
HYB_209	7290	0.2024%
HYB_210	8740	0.2663%

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	0.06%	0.19%	60.94
ANG_302	0.08%	0.29%	58.08
ANG_303	0.06%	0.21%	58.23
ANG_304	0.06%	0.22%	59.56
ANG_305	0.06%	0.22%	57.12
ANG_307	0.06%	0.20%	58.15
ANG_308	0.05%	0.19%	58.21
ANG_401	0.07%	0.24%	56.86
ANG_402	0.06%	0.20%	55.69
ANG_403	0.07%	0.27%	53.36
ANG_404	0.07%	0.25%	55.12
ANG_407	0.06%	0.21%	54.91
ANG_501	0.07%	0.26%	55.18
ANG_503	0.11%	0.41%	51.42
ANG_505	0.08%	0.30%	51.48
ANG_506	0.07%	0.24%	58.43
CHAR_601	0.21%	0.69%	60.54
CHAR_604	0.12%	0.41%	56.91
CHAR_608	0.08%	0.30%	55.24
CHAR_611	0.07%	0.24%	55.91
CHAR_612	0.08%	0.28%	56.93
CHAR_701	0.08%	0.29%	57.24
CHAR_702	0.13%	0.43%	60.98
CHAR_703	0.07%	0.25%	57.05
CHAR_704	0.06%	0.20%	58.31
CHAR_705	0.06%	0.21%	57.48
CHAR_706	0.07%	0.25%	55.29
CHAR_707	0.08%	0.27%	57.05
CHAR_708	0.09%	0.35%	52.95
CHAR_709	0.12%	0.41%	57.65
CHAR_710	0.08%	0.30%	55.35
CHAR_712	0.08%	0.32%	51.05
HYB_101	0.06%	0.19%	58.76
HYB_103	0.07%	0.23%	57.70
HYB_104	0.08%	0.25%	58.91
HYB_105	0.07%	0.23%	56.71
HYB_106	0.07%	0.25%	56.67
HYB_107	0.07%	0.25%	59.89
HYB_112	0.07%	0.24%	56.63
HYB_201	0.06%	0.21%	58.19
HYB_202	0.09%	0.31%	58.13
HYB_203	0.07%	0.24%	59.89
HYB_205	0.06%	0.21%	58.95
HYB_206	0.08%	0.28%	59.76
HYB_207	0.08%	0.25%	59.00
HYB_208	0.07%	0.26%	55.93
HYB_209	0.06%	0.23%	55.49
HYB_210	0.07%	0.25%	56.01

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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_QWindowTrim

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

Showing ⁴⁸/₄₈ rows and ⁵/₅ columns.

Sample Name	% Bp Lost	% R1 of Bp Lost	% R2 of Bp Lost	Avg. Bps Trimmed
ANG_301	2.58%	16.58%	83.42%	5.16
ANG_302	3.00%	17.46%	82.54%	5.99
ANG_303	4.52%	22.10%	77.90%	9.04
ANG_304	4.20%	21.26%	78.74%	8.39
ANG_305	4.25%	21.38%	78.62%	8.49
ANG_307	4.70%	20.57%	79.43%	9.39
ANG_308	4.76%	18.92%	81.08%	9.52
ANG_401	5.86%	16.53%	83.47%	11.71
ANG_402	6.89%	14.68%	85.32%	13.78
ANG_403	4.75%	19.73%	80.27%	9.50
ANG_404	7.17%	15.20%	84.80%	14.33
ANG_407	6.16%	17.10%	82.90%	12.32
ANG_501	6.33%	15.16%	84.84%	12.65
ANG_503	7.04%	14.82%	85.18%	14.07
ANG_505	4.05%	15.23%	84.77%	8.10
ANG_506	6.43%	10.66%	89.34%	12.84
CHAR_601	4.77%	13.21%	86.79%	9.52
CHAR_604	4.79%	12.84%	87.16%	9.57
CHAR_608	8.20%	8.40%	91.60%	16.39
CHAR_611	6.96%	10.24%	89.76%	13.91
CHAR_612	7.08%	10.39%	89.61%	14.16
CHAR_701	8.60%	9.27%	90.73%	17.19
CHAR_702	6.64%	10.17%	89.83%	13.27
CHAR_703	6.38%	11.21%	88.79%	12.75
CHAR_704	5.25%	12.77%	87.23%	10.50
CHAR_705	4.08%	16.63%	83.37%	8.15
CHAR_706	7.28%	8.23%	91.77%	14.55
CHAR_707	2.42%	20.05%	79.95%	4.84
CHAR_708	2.56%	19.68%	80.32%	5.12
CHAR_709	6.37%	10.79%	89.21%	12.73
CHAR_710	3.20%	17.97%	82.03%	6.39
CHAR_712	3.27%	17.06%	82.94%	6.54
HYB_101	3.57%	18.99%	81.01%	7.14
HYB_103	3.87%	19.24%	80.76%	7.73
HYB_104	3.56%	20.47%	79.53%	7.11
HYB_105	5.36%	12.54%	87.46%	10.71
HYB_106	6.15%	10.86%	89.14%	12.29
HYB_107	3.49%	18.46%	81.54%	6.97
HYB_112	3.93%	10.75%	89.25%	7.86
HYB_201	4.73%	9.37%	90.63%	9.45
HYB_202	5.24%	8.95%	91.05%	10.47
HYB_203	2.76%	15.98%	84.02%	5.51
HYB_205	2.61%	16.56%	83.44%	5.21
HYB_206	2.69%	16.94%	83.06%	5.37
HYB_207	2.87%	17.88%	82.12%	5.74
HYB_208	5.11%	11.53%	88.47%	10.21
HYB_209	4.14%	12.02%	87.98%	8.27
HYB_210	4.90%	11.21%	88.79%	9.80

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
\|\|	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 ³/₃ columns.

Sample Name	% PE Lost	% PE Orphaned
ANG_301	3.98%	3.73%
ANG_302	4.70%	4.36%
ANG_303	6.47%	5.90%
ANG_304	6.07%	5.57%
ANG_305	6.15%	5.65%
ANG_307	6.85%	6.30%
ANG_308	7.18%	6.69%
ANG_401	9.24%	8.65%
ANG_402	11.24%	10.67%
ANG_403	7.19%	6.69%
ANG_404	11.72%	11.07%
ANG_407	9.74%	9.13%
ANG_501	10.32%	9.76%
ANG_503	11.66%	11.03%
ANG_505	6.54%	6.18%
ANG_506	11.12%	10.75%
CHAR_601	8.19%	7.73%
CHAR_604	8.12%	7.77%
CHAR_608	14.71%	14.32%
CHAR_611	12.08%	11.67%
CHAR_612	12.37%	11.94%
CHAR_701	15.32%	14.83%
CHAR_702	11.77%	11.35%
CHAR_703	10.98%	10.58%
CHAR_704	8.80%	8.47%
CHAR_705	6.46%	6.12%
CHAR_706	13.12%	12.80%
CHAR_707	3.59%	3.34%
CHAR_708	3.86%	3.58%
CHAR_709	11.16%	10.79%
CHAR_710	4.94%	4.60%
CHAR_712	5.14%	4.83%
HYB_101	5.32%	4.93%
HYB_103	5.80%	5.36%
HYB_104	5.25%	4.84%
HYB_105	9.05%	8.66%
HYB_106	10.68%	10.31%
HYB_107	5.29%	4.91%
HYB_112	6.82%	6.57%
HYB_201	8.34%	8.08%
HYB_202	9.40%	9.12%
HYB_203	4.34%	4.06%
HYB_205	4.06%	3.82%
HYB_206	4.23%	3.92%
HYB_207	4.47%	4.15%
HYB_208	8.86%	8.54%
HYB_209	7.01%	6.71%
HYB_210	8.51%	8.19%

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 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
\|\|	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	96.26%	3.74%	96.18%	94.28%	71.17%	45.29%	0.0041%
ANG_302	95.62%	4.38%	95.94%	93.88%	71.63%	47.19%	0.0040%
ANG_303	94.07%	5.93%	92.02%	89.93%	65.76%	47.43%	0.0049%
ANG_304	94.40%	5.60%	92.60%	90.57%	66.92%	46.28%	0.0050%
ANG_305	94.32%	5.68%	92.53%	90.54%	66.68%	46.67%	0.0049%
ANG_307	93.67%	6.33%	92.30%	89.80%	65.98%	47.13%	0.0047%
ANG_308	93.28%	6.72%	92.44%	90.45%	71.36%	46.92%	0.0051%
ANG_401	91.30%	8.70%	92.39%	89.79%	73.20%	46.98%	0.0051%
ANG_402	89.27%	10.73%	92.16%	89.51%	76.90%	47.98%	0.0047%
ANG_403	93.28%	6.72%	92.36%	90.57%	72.11%	47.84%	0.0048%
ANG_404	88.86%	11.14%	92.03%	89.51%	77.46%	48.20%	0.0047%
ANG_407	90.81%	9.19%	92.04%	89.58%	74.81%	49.00%	0.0047%
ANG_501	90.18%	9.82%	92.49%	90.46%	78.39%	46.19%	0.0049%
ANG_503	88.90%	11.10%	92.48%	90.49%	79.95%	46.22%	0.0050%
ANG_505	93.79%	6.21%	95.39%	93.99%	81.02%	46.15%	0.0033%
ANG_506	89.21%	10.79%	94.81%	92.97%	85.50%	46.94%	0.0033%
CHAR_601	92.23%	7.77%	95.69%	94.54%	85.89%	41.04%	0.0033%
CHAR_604	92.21%	7.79%	95.61%	94.30%	85.42%	42.47%	0.0034%
CHAR_608	85.63%	14.37%	94.95%	92.79%	87.31%	44.91%	0.0033%
CHAR_611	88.28%	11.72%	94.94%	92.61%	84.78%	47.00%	0.0033%
CHAR_612	88.01%	11.99%	94.28%	92.14%	84.15%	46.43%	0.0023%
CHAR_701	85.10%	14.90%	94.04%	91.85%	85.74%	46.98%	0.0022%
CHAR_702	88.60%	11.40%	94.64%	93.00%	85.82%	43.02%	0.0022%
CHAR_703	89.37%	10.63%	94.30%	92.39%	83.81%	46.94%	0.0022%
CHAR_704	91.51%	8.49%	94.26%	92.78%	82.10%	47.82%	0.0022%
CHAR_705	93.86%	6.14%	94.31%	93.06%	78.48%	47.83%	0.0022%
CHAR_706	87.16%	12.84%	95.29%	93.63%	88.47%	47.31%	0.0020%
CHAR_707	96.65%	3.35%	95.66%	94.50%	73.11%	47.12%	0.0020%
CHAR_708	96.41%	3.59%	95.66%	94.57%	73.49%	47.02%	0.0019%
CHAR_709	89.17%	10.83%	95.62%	94.14%	87.68%	45.30%	0.0020%
CHAR_710	95.39%	4.61%	95.41%	93.82%	74.50%	48.37%	0.0019%
CHAR_712	95.16%	4.84%	95.34%	94.04%	77.48%	46.80%	0.0019%
HYB_101	95.05%	4.95%	94.60%	92.42%	68.79%	47.15%	0.0091%
HYB_103	94.61%	5.39%	94.63%	92.38%	69.45%	47.48%	0.0090%
HYB_104	95.14%	4.86%	94.46%	92.68%	69.88%	46.99%	0.0092%
HYB_105	91.31%	8.69%	94.63%	92.85%	82.81%	47.21%	0.0092%
HYB_106	89.65%	10.35%	94.61%	92.99%	85.41%	47.57%	0.0092%
HYB_107	95.07%	4.93%	94.84%	92.92%	70.57%	45.78%	0.0090%
HYB_112	93.41%	6.59%	96.34%	94.91%	86.19%	46.98%	0.0036%
HYB_201	91.89%	8.11%	96.36%	94.57%	86.84%	47.26%	0.0034%
HYB_202	90.85%	9.15%	96.40%	94.79%	88.33%	45.84%	0.0035%
HYB_203	95.93%	4.07%	96.39%	94.42%	72.52%	47.04%	0.0035%
HYB_205	96.17%	3.83%	96.43%	94.63%	73.05%	46.55%	0.0034%
HYB_206	96.07%	3.93%	96.41%	94.49%	72.40%	46.34%	0.0035%
HYB_207	95.84%	4.16%	95.93%	94.05%	71.65%	47.38%	0.0040%
HYB_208	91.43%	8.57%	95.71%	94.22%	86.57%	48.75%	0.0041%
HYB_209	93.27%	6.73%	96.01%	93.92%	82.19%	48.17%	0.0041%
HYB_210	91.79%	8.21%	95.53%	93.79%	84.91%	48.94%	0.0041%

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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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