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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 1.10.1

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

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

This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation.

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Report generated on 2024-05-23, 13:21 based on data in: /projects/tomato_genome/fnb/dataprocessing/SRP460750/nfcore-SL4-2024-05-21/work/65/174cf043d42197f8695f1bc1fa387d

General Statistics

Showing ²¹⁶/₂₁₆ rows and ¹⁵/₁₉ columns.

Sample Name	M Reads	M Reads Mapped	dupInt	% Proper Pairs	Error rate	M Non-Primary	M Reads Mapped	% Mapped	% Proper Pairs	% MapQ 0 Reads	M Total seqs	% Aligned	M Aligned	% BP Trimmed	% Dups	% GC	Length	% Failed	M Seqs
SRR25478240	78.6	78.6	0.00%	87.4%	0.22%	6.1	72.5	100.0%	100.0%	0.2%	72.5	93.2%	34.3
SRR25478240_1														1.4%	88.3%	41%	148 bp	18%	36.8
SRR25478240_2														1.3%	89.1%	40%	148 bp	18%	36.8
SRR25478241	75.8	75.8	0.00%	87.6%	0.25%	5.8	70.1	100.0%	100.0%	0.2%	70.1	93.2%	33.2
SRR25478241_1														1.5%	87.1%	41%	148 bp	18%	35.6
SRR25478241_2														1.4%	87.4%	40%	147 bp	18%	35.6
SRR25478242	76.2	76.2	0.00%	87.6%	0.24%	5.8	70.4	100.0%	100.0%	0.2%	70.4	93.6%	33.4
SRR25478242_1														2.3%	88.2%	41%	147 bp	18%	35.7
SRR25478242_2														1.9%	88.0%	40%	147 bp	18%	35.7
SRR25478243	67.8	67.8	0.00%	88.0%	0.23%	5.0	62.8	100.0%	100.0%	0.2%	62.8	93.8%	29.8
SRR25478243_1														1.5%	87.6%	41%	147 bp	18%	31.8
SRR25478243_2														1.6%	87.5%	40%	147 bp	18%	31.8
SRR25478244	75.0	75.0	0.00%	87.7%	0.26%	5.6	69.4	100.0%	100.0%	0.2%	69.4	93.2%	32.9
SRR25478244_1														1.5%	87.4%	41%	148 bp	18%	35.3
SRR25478244_2														1.4%	87.0%	40%	147 bp	18%	35.3
SRR25478245	89.3	89.3	0.00%	87.6%	0.25%	6.7	82.6	100.0%	100.0%	0.1%	82.6	93.0%	39.1
SRR25478245_1														1.4%	89.0%	41%	148 bp	18%	42.0
SRR25478245_2														1.4%	88.8%	40%	147 bp	18%	42.0
SRR25478246	80.8	80.8	0.00%	87.7%	0.25%	6.0	74.8	100.0%	100.0%	0.1%	74.8	92.9%	35.5
SRR25478246_1														1.7%	88.9%	41%	147 bp	18%	38.2
SRR25478246_2														1.6%	88.8%	40%	147 bp	18%	38.2
SRR25478247	68.3	68.3	0.00%	87.9%	0.25%	5.0	63.3	100.0%	100.0%	0.1%	63.3	93.7%	30.0
SRR25478247_1														1.8%	88.7%	41%	147 bp	18%	32.0
SRR25478247_2														1.7%	87.9%	40%	147 bp	18%	32.0
SRR25478248	76.4	76.4	0.00%	87.5%	0.24%	5.7	70.6	100.0%	100.0%	0.1%	70.6	93.4%	33.4
SRR25478248_1														1.4%	89.2%	41%	148 bp	18%	35.7
SRR25478248_2														1.3%	88.7%	40%	148 bp	18%	35.7
SRR25478249	73.0	73.0	0.00%	87.6%	0.26%	5.4	67.6	100.0%	100.0%	0.1%	67.6	93.3%	32.0
SRR25478249_1														1.9%	88.3%	41%	147 bp	18%	34.3
SRR25478249_2														1.6%	88.2%	40%	147 bp	18%	34.3
SRR25478250	89.5	89.5	0.00%	86.5%	0.25%	7.4	82.1	100.0%	100.0%	0.3%	82.1	91.1%	38.7
SRR25478250_1														1.7%	88.5%	41%	147 bp	18%	42.5
SRR25478250_2														1.5%	88.2%	40%	147 bp	18%	42.5
SRR25478251	89.9	89.9	0.00%	87.1%	0.24%	7.0	82.9	100.0%	100.0%	0.2%	82.9	93.3%	39.2
SRR25478251_1														1.5%	89.1%	41%	147 bp	18%	42.0
SRR25478251_2														1.6%	88.6%	40%	147 bp	18%	42.0
SRR25478252	75.1	75.1	0.00%	87.6%	0.25%	5.7	69.4	100.0%	100.0%	0.2%	69.4	87.7%	32.9
SRR25478252_1														1.9%	88.8%	42%	147 bp	18%	37.5
SRR25478252_2														1.9%	88.6%	41%	147 bp	18%	37.5
SRR25478253	87.8	87.8	0.00%	87.0%	0.25%	7.0	80.8	100.0%	100.0%	0.2%	80.8	93.2%	38.2
SRR25478253_1														1.5%	88.7%	41%	147 bp	18%	41.0
SRR25478253_2														1.5%	88.2%	40%	147 bp	18%	41.0
SRR25478254	80.9	80.9	0.00%	86.7%	0.22%	6.6	74.4	100.0%	100.0%	0.2%	74.4	92.8%	35.1
SRR25478254_1														1.4%	88.6%	42%	148 bp	18%	37.8
SRR25478254_2														1.5%	88.6%	41%	147 bp	18%	37.8
SRR25478255	88.3	88.3	0.00%	87.5%	0.25%	6.8	81.4	100.0%	100.0%	0.3%	81.4	92.9%	38.6
SRR25478255_1														1.5%	88.1%	41%	148 bp	18%	41.5
SRR25478255_2														1.5%	87.2%	40%	147 bp	18%	41.5
SRR25478256	73.6	73.6	0.00%	87.9%	0.25%	5.5	68.2	100.0%	100.0%	0.2%	68.2	93.1%	32.4
SRR25478256_1														1.8%	86.9%	41%	147 bp	18%	34.8
SRR25478256_2														1.7%	86.4%	40%	147 bp	18%	34.8
SRR25478257	71.1	71.1	0.00%	87.8%	0.23%	5.3	65.8	100.0%	100.0%	0.2%	65.8	93.2%	31.2
SRR25478257_1														1.9%	87.4%	41%	147 bp	18%	33.5
SRR25478257_2														1.6%	86.9%	40%	147 bp	18%	33.5
SRR25478258	80.8	80.8	0.00%	87.7%	0.26%	6.2	74.6	100.0%	100.0%	0.3%	74.6	92.8%	35.4
SRR25478258_1														1.6%	87.6%	41%	147 bp	18%	38.1
SRR25478258_2														1.6%	86.4%	40%	147 bp	18%	38.1
SRR25478259	77.6	77.6	0.00%	87.8%	0.23%	5.8	71.9	100.0%	100.0%	0.2%	71.9	93.1%	34.1
SRR25478259_1														1.4%	88.6%	41%	148 bp	18%	36.6
SRR25478259_2														1.4%	89.2%	40%	147 bp	18%	36.6
SRR25478260	75.1	75.1	0.00%	87.6%	0.23%	5.7	69.5	100.0%	100.0%	0.1%	69.5	93.3%	32.9
SRR25478260_1														1.5%	88.4%	41%	148 bp	18%	35.3
SRR25478260_2														1.5%	89.0%	40%	147 bp	18%	35.3
SRR25478261	77.5	77.5	0.00%	87.5%	0.21%	5.9	71.6	100.0%	100.0%	0.2%	71.6	92.6%	33.9
SRR25478261_1														1.9%	88.8%	41%	147 bp	18%	36.6
SRR25478261_2														1.6%	89.6%	40%	147 bp	18%	36.6
SRR25478262	88.3	88.3	0.00%	87.5%	0.23%	6.7	81.6	100.0%	100.0%	0.2%	81.6	93.4%	38.6
SRR25478262_1														1.4%	89.2%	41%	148 bp	18%	41.3
SRR25478262_2														1.4%	89.7%	40%	147 bp	18%	41.3
SRR25478263	75.1	75.1	0.00%	88.1%	0.22%	5.4	69.7	100.0%	100.0%	0.1%	69.7	93.9%	33.1
SRR25478263_1														1.7%	89.1%	41%	147 bp	18%	35.2
SRR25478263_2														1.6%	89.1%	40%	147 bp	18%	35.2
SRR25478264	72.5	72.5	0.00%	87.7%	0.27%	5.4	67.1	100.0%	100.0%	0.1%	67.1	93.3%	31.8
SRR25478264_1														1.4%	88.6%	41%	148 bp	18%	34.0
SRR25478264_2														1.4%	87.8%	40%	147 bp	18%	34.0
SRR25478265	82.0	82.0	0.00%	87.7%	0.24%	6.1	75.9	100.0%	100.0%	0.1%	75.9	93.5%	36.0
SRR25478265_1														1.4%	89.1%	41%	148 bp	18%	38.5
SRR25478265_2														1.3%	89.5%	40%	148 bp	18%	38.5
SRR25478266	82.1	82.1	0.00%	88.0%	0.23%	5.9	76.2	100.0%	100.0%	0.1%	76.2	93.8%	36.1
SRR25478266_1														1.6%	89.3%	41%	147 bp	18%	38.6
SRR25478266_2														1.6%	88.9%	40%	147 bp	18%	38.6
SRR25478267	69.1	69.1	0.00%	88.1%	0.22%	5.0	64.1	100.0%	100.0%	0.1%	64.1	93.9%	30.4
SRR25478267_1														2.1%	88.8%	41%	147 bp	18%	32.4
SRR25478267_2														1.8%	88.5%	40%	147 bp	18%	32.4
SRR25478268	66.8	66.8	0.00%	87.6%	0.22%	5.0	61.7	100.0%	100.0%	0.2%	61.7	90.7%	29.3
SRR25478268_1														2.1%	89.0%	42%	147 bp	18%	32.3
SRR25478268_2														1.9%	88.9%	41%	147 bp	18%	32.3
SRR25478269	70.1	70.1	0.00%	87.9%	0.26%	5.1	65.0	100.0%	100.0%	0.1%	65.0	93.7%	30.8
SRR25478269_1														2.0%	88.4%	41%	147 bp	18%	32.9
SRR25478269_2														1.8%	87.4%	40%	147 bp	18%	32.9
SRR25478270	73.7	73.7	0.00%	87.9%	0.26%	5.3	68.4	100.0%	100.0%	0.1%	68.4	93.3%	32.4
SRR25478270_1														1.4%	88.8%	41%	148 bp	18%	34.8
SRR25478270_2														1.4%	88.2%	40%	147 bp	18%	34.8
SRR25478271	85.6	85.6	0.00%	87.9%	0.22%	6.3	79.4	100.0%	100.0%	0.1%	79.4	93.7%	37.6
SRR25478271_1														2.3%	89.3%	41%	147 bp	18%	40.2
SRR25478271_2														1.8%	89.7%	40%	147 bp	18%	40.2
SRR25478272	79.0	79.0	0.00%	87.5%	0.26%	5.9	73.1	100.0%	100.0%	0.1%	73.1	92.2%	34.6
SRR25478272_1														1.8%	87.7%	41%	147 bp	18%	37.6
SRR25478272_2														1.6%	87.4%	40%	147 bp	18%	37.6
SRR25478273	74.5	74.5	0.00%	87.7%	0.24%	5.5	69.0	100.0%	100.0%	0.1%	69.0	92.8%	32.7
SRR25478273_1														1.9%	88.3%	41%	147 bp	18%	35.2
SRR25478273_2														1.6%	87.7%	40%	147 bp	18%	35.2
SRR25478274	94.2	94.2	0.00%	87.9%	0.27%	6.9	87.3	100.0%	100.0%	0.1%	87.3	92.9%	41.4
SRR25478274_1														1.7%	88.8%	41%	147 bp	18%	44.5
SRR25478274_2														1.6%	87.5%	40%	147 bp	18%	44.5
SRR25478275	73.2	73.2	0.00%	87.9%	0.23%	5.4	67.8	100.0%	100.0%	0.1%	67.8	93.0%	32.1
SRR25478275_1														2.1%	88.6%	42%	147 bp	18%	34.6
SRR25478275_2														1.8%	87.9%	40%	147 bp	18%	34.6
SRR25478276	92.1	92.1	0.00%	87.7%	0.25%	6.9	85.2	100.0%	100.0%	0.1%	85.2	92.9%	40.4
SRR25478276_1														1.5%	89.7%	41%	148 bp	18%	43.5
SRR25478276_2														1.5%	89.1%	40%	147 bp	18%	43.5
SRR25478277	94.6	94.6	0.00%	87.7%	0.25%	7.1	87.5	100.0%	100.0%	0.1%	87.5	93.6%	41.5
SRR25478277_1														1.5%	89.4%	41%	147 bp	18%	44.3
SRR25478277_2														1.5%	88.7%	40%	147 bp	18%	44.3
SRR25478278	88.8	88.8	0.00%	87.6%	0.23%	6.7	82.1	100.0%	100.0%	0.1%	82.1	92.9%	38.9
SRR25478278_1														1.8%	89.7%	41%	147 bp	18%	41.9
SRR25478278_2														1.7%	89.4%	40%	147 bp	18%	41.9
SRR25478279	93.3	93.3	0.00%	87.8%	0.26%	6.9	86.4	100.0%	100.0%	0.1%	86.4	93.5%	41.0
SRR25478279_1														1.4%	89.5%	41%	148 bp	18%	43.8
SRR25478279_2														1.5%	88.6%	40%	147 bp	18%	43.8
SRR25478280	74.5	74.5	0.00%	87.7%	0.29%	5.5	69.0	100.0%	100.0%	0.1%	69.0	93.3%	32.7
SRR25478280_1														1.7%	88.8%	41%	148 bp	18%	35.0
SRR25478280_2														1.5%	87.1%	40%	147 bp	18%	35.0
SRR25478281	69.8	69.8	0.00%	87.9%	0.24%	5.1	64.7	100.0%	100.0%	0.1%	64.7	93.7%	30.7
SRR25478281_1														1.9%	89.0%	41%	147 bp	18%	32.7
SRR25478281_2														1.7%	88.3%	40%	147 bp	18%	32.7
SRR25478282	71.8	71.8	0.00%	88.1%	0.22%	5.1	66.7	100.0%	100.0%	0.1%	66.7	93.7%	31.7
SRR25478282_1														1.7%	89.0%	41%	147 bp	18%	33.8
SRR25478282_2														1.5%	89.4%	40%	147 bp	18%	33.8
SRR25478283	67.1	67.1	0.00%	87.8%	0.20%	5.0	62.1	100.0%	100.0%	0.1%	62.1	93.9%	29.5
SRR25478283_1														2.0%	89.0%	41%	147 bp	18%	31.4
SRR25478283_2														1.8%	89.3%	40%	147 bp	18%	31.4
SRR25478284	92.6	92.6	0.00%	87.7%	0.28%	6.8	85.8	100.0%	100.0%	0.1%	85.8	93.3%	40.6
SRR25478284_1														1.6%	89.5%	41%	147 bp	18%	43.5
SRR25478284_2														1.6%	87.9%	40%	147 bp	18%	43.5
SRR25478285	74.4	74.4	0.00%	88.2%	0.22%	5.3	69.1	100.0%	100.0%	0.1%	69.1	93.9%	32.8
SRR25478285_1														1.8%	88.8%	41%	147 bp	18%	34.9
SRR25478285_2														1.6%	89.1%	40%	147 bp	18%	34.9
SRR25478286	77.9	77.9	0.00%	88.0%	0.27%	5.6	72.4	100.0%	100.0%	0.1%	72.4	93.5%	34.3
SRR25478286_1														1.5%	88.8%	41%	148 bp	18%	36.7
SRR25478286_2														1.5%	87.7%	40%	147 bp	18%	36.7
SRR25478287	75.4	75.4	0.00%	87.2%	0.25%	5.9	69.5	100.0%	100.0%	0.3%	69.5	93.4%	32.9
SRR25478287_1														1.4%	87.5%	41%	148 bp	18%	35.2
SRR25478287_2														1.4%	87.4%	40%	147 bp	18%	35.2
SRR25478288	69.5	69.5	0.00%	88.1%	0.24%	5.0	64.5	100.0%	100.0%	0.1%	64.5	93.6%	30.6
SRR25478288_1														1.5%	87.6%	41%	148 bp	18%	32.7
SRR25478288_2														1.4%	88.0%	40%	147 bp	18%	32.7
SRR25478289	75.5	75.5	0.00%	87.6%	0.20%	5.7	69.8	100.0%	100.0%	0.1%	69.8	93.7%	33.1
SRR25478289_1														2.0%	88.9%	42%	147 bp	18%	35.3
SRR25478289_2														1.9%	89.1%	41%	147 bp	18%	35.3
SRR25478290	79.8	79.8	0.00%	87.8%	0.25%	5.8	73.9	100.0%	100.0%	0.1%	73.9	93.6%	35.0
SRR25478290_1														1.5%	88.7%	41%	148 bp	18%	37.4
SRR25478290_2														1.5%	88.4%	40%	147 bp	18%	37.4
SRR25478291	70.7	70.7	0.00%	88.1%	0.26%	5.1	65.6	100.0%	100.0%	0.1%	65.6	93.7%	31.1
SRR25478291_1														1.4%	88.0%	41%	148 bp	18%	33.2
SRR25478291_2														1.4%	87.8%	40%	148 bp	18%	33.2
SRR25478292	58.9	58.9	0.00%	87.9%	0.21%	4.4	54.5	100.0%	100.0%	0.1%	54.5	91.3%	25.9
SRR25478292_1														2.2%	88.2%	42%	147 bp	18%	28.3
SRR25478292_2														1.9%	88.5%	41%	147 bp	18%	28.3
SRR25478293	79.2	79.2	0.00%	87.0%	0.27%	6.2	73.0	100.0%	100.0%	0.2%	73.0	92.6%	34.5
SRR25478293_1														1.3%	87.9%	41%	148 bp	18%	37.2
SRR25478293_2														1.2%	87.5%	40%	148 bp	18%	37.2
SRR25478294	84.2	84.2	0.00%	87.6%	0.25%	6.4	77.8	100.0%	100.0%	0.2%	77.8	93.5%	36.9
SRR25478294_1														1.5%	88.9%	41%	148 bp	18%	39.4
SRR25478294_2														1.5%	87.9%	40%	147 bp	18%	39.4
SRR25478295	75.1	75.1	0.00%	87.2%	0.24%	5.9	69.2	100.0%	100.0%	0.2%	69.2	93.2%	32.8
SRR25478295_1														1.6%	88.4%	41%	147 bp	18%	35.2
SRR25478295_2														1.6%	88.0%	40%	147 bp	18%	35.2
SRR25478296	77.3	77.3	0.00%	87.7%	0.23%	5.9	71.5	100.0%	100.0%	0.2%	71.5	93.9%	33.9
SRR25478296_1														1.7%	88.3%	41%	147 bp	18%	36.2
SRR25478296_2														1.5%	88.0%	40%	147 bp	18%	36.2
SRR25478297	75.7	75.7	0.00%	87.3%	0.24%	6.0	69.7	100.0%	100.0%	0.3%	69.7	93.5%	33.0
SRR25478297_1														1.4%	87.6%	41%	148 bp	18%	35.3
SRR25478297_2														1.4%	87.8%	40%	147 bp	18%	35.3
SRR25478298	81.6	81.6	0.00%	87.3%	0.24%	6.4	75.2	100.0%	100.0%	0.3%	75.2	93.4%	35.6
SRR25478298_1														2.1%	87.8%	41%	147 bp	18%	38.2
SRR25478298_2														1.8%	87.8%	40%	147 bp	18%	38.2
SRR25478299	80.7	80.7	0.00%	87.7%	0.22%	6.1	74.6	100.0%	100.0%	0.2%	74.6	93.7%	35.4
SRR25478299_1														2.0%	88.9%	42%	147 bp	18%	37.8
SRR25478299_2														1.8%	88.6%	40%	147 bp	18%	37.8
SRR25478300	65.3	65.3	0.00%	88.0%	0.21%	4.8	60.5	100.0%	100.0%	0.2%	60.5	93.9%	28.7
SRR25478300_1														2.1%	88.4%	42%	147 bp	18%	30.6
SRR25478300_2														1.9%	88.3%	40%	147 bp	18%	30.6
SRR25478301	77.9	77.9	0.00%	88.0%	0.26%	5.8	72.2	100.0%	100.0%	0.2%	72.2	93.7%	34.3
SRR25478301_1														1.5%	87.9%	41%	148 bp	18%	36.6
SRR25478301_2														1.5%	87.3%	40%	147 bp	18%	36.6
SRR25478302	74.5	74.5	0.00%	87.7%	0.22%	5.6	68.8	100.0%	100.0%	0.2%	68.8	93.7%	32.7
SRR25478302_1														2.0%	88.7%	42%	147 bp	18%	34.9
SRR25478302_2														1.8%	88.5%	41%	147 bp	18%	34.9
SRR25478303	78.1	78.1	0.00%	88.2%	0.25%	5.6	72.5	100.0%	100.0%	0.1%	72.5	93.8%	34.5
SRR25478303_1														1.5%	88.4%	41%	147 bp	18%	36.8
SRR25478303_2														1.6%	88.1%	40%	147 bp	18%	36.8
SRR25478304	67.2	67.2	0.00%	87.8%	0.23%	5.0	62.3	100.0%	100.0%	0.1%	62.3	92.4%	29.5
SRR25478304_1														1.6%	88.0%	41%	148 bp	18%	32.0
SRR25478304_2														1.5%	88.4%	40%	147 bp	18%	32.0
SRR25478305	69.2	69.2	0.00%	88.0%	0.22%	5.1	64.1	100.0%	100.0%	0.1%	64.1	94.0%	30.4
SRR25478305_1														1.6%	88.2%	41%	147 bp	18%	32.4
SRR25478305_2														1.6%	88.4%	40%	147 bp	18%	32.4
SRR25478306	74.3	74.3	0.00%	87.6%	0.24%	5.6	68.7	100.0%	100.0%	0.1%	68.7	93.5%	32.6
SRR25478306_1														1.5%	88.4%	41%	148 bp	18%	34.8
SRR25478306_2														1.5%	88.3%	40%	147 bp	18%	34.8
SRR25478307	73.0	73.0	0.00%	87.7%	0.27%	5.4	67.6	100.0%	100.0%	0.1%	67.6	93.3%	32.0
SRR25478307_1														1.4%	88.7%	41%	148 bp	18%	34.3
SRR25478307_2														1.4%	88.1%	40%	147 bp	18%	34.3
SRR25478308	83.3	83.3	0.00%	87.8%	0.27%	6.1	77.3	100.0%	100.0%	0.1%	77.3	93.4%	36.6
SRR25478308_1														1.5%	89.1%	41%	148 bp	18%	39.2
SRR25478308_2														1.5%	88.4%	40%	147 bp	18%	39.2
SRR25478309	73.0	73.0	0.00%	87.5%	0.27%	5.5	67.5	100.0%	100.0%	0.1%	67.5	93.4%	31.9
SRR25478309_1														1.8%	89.0%	41%	147 bp	18%	34.2
SRR25478309_2														1.6%	87.5%	40%	147 bp	18%	34.2
SRR25478310	81.5	81.5	0.00%	88.0%	0.27%	5.8	75.6	100.0%	100.0%	0.1%	75.6	93.6%	35.9
SRR25478310_1														2.1%	88.7%	41%	147 bp	18%	38.3
SRR25478310_2														1.7%	87.7%	40%	147 bp	18%	38.3
SRR25478311	81.1	81.1	0.00%	87.6%	0.29%	6.0	75.1	100.0%	100.0%	0.1%	75.1	93.2%	35.5
SRR25478311_1														1.6%	88.7%	41%	148 bp	18%	38.1
SRR25478311_2														1.5%	87.4%	40%	147 bp	18%	38.1

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

Sort	Group	Column	Description	ID	Scale
\|\|	Samtools	M Reads	Total reads in the bam file (millions)	`flagstat_total`	read_count
\|\|	Samtools	M Reads Mapped	Reads Mapped in the bam file (millions)	`mapped_passed`	read_count
\|\|	DupRadar	dupInt	Intercept value from DupRadar	`dupRadar_intercept`	None
\|\|	RSeQC	% Proper Pairs	% Reads mapped in proper pairs	`proper_pairs_percent`	None
\|\|	Samtools	Error rate	Error rate: mismatches (NM) / bases mapped (CIGAR)	`error_rate`	None
\|\|	Samtools	M Non-Primary	Non-primary alignments (millions)	`non-primary_alignments`	read_count
\|\|	Samtools	M Reads Mapped	Reads Mapped in the bam file (millions)	`reads_mapped`	read_count
\|\|	Samtools	% Mapped	% Mapped Reads	`reads_mapped_percent`	None
\|\|	Samtools	% Proper Pairs	% Properly Paired Reads	`reads_properly_paired_percent`	None
\|\|	Samtools	% MapQ 0 Reads	% of Reads that are Ambiguously Placed (MapQ=0)	`reads_MQ0_percent`	None
\|\|	Samtools	M Total seqs	Total sequences in the bam file (millions)	`raw_total_sequences`	read_count
\|\|	STAR	% Aligned	% Uniquely mapped reads	`uniquely_mapped_percent`	None
\|\|	STAR	M Aligned	Uniquely mapped reads (millions)	`uniquely_mapped`	read_count
\|\|	Cutadapt	% BP Trimmed	% Total Base Pairs trimmed	`percent_trimmed`	None
\|\|	FastQC (trimmed)	% Dups	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC (trimmed)	% GC	Average % GC Content	`percent_gc`	None
\|\|	FastQC (trimmed)	Length	Average Sequence Length (bp)	`avg_sequence_length`	None
\|\|	FastQC (trimmed)	% Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	FastQC (trimmed)	M Seqs	Total Sequences (millions)	`total_sequences`	read_count

STAR_SALMON DESeq2 PCA plot

PCA plot between samples in the experiment. These values are calculated using DESeq2 in the deseq2_qc.r script.

STAR_SALMON DESeq2 sample similarity

is generated from clustering by Euclidean distances between DESeq2 rlog values for each sample in the deseq2_qc.r script.

DupRadar

provides duplication rate quality control for RNA-Seq datasets. Highly expressed genes can be expected to have a lot of duplicate reads, but high numbers of duplicates at low read counts can indicate low library complexity with technical duplication. This plot shows the general linear models - a summary of the gene duplication distributions.

Preseq

Preseq estimates the complexity of a library, showing how many additional unique reads are sequenced for increasing total read count. A shallow curve indicates complexity saturation. The dashed line shows a perfectly complex library where total reads = unique reads.

Complexity curve

Note that the x axis is trimmed at the point where all the datasets show 80% of their maximum y-value, to avoid ridiculous scales.

RSeQC

RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput RNA-seq data.

Read Distribution

Read Distribution calculates how mapped reads are distributed over genome features.

Inner Distance

Inner Distance calculates the inner distance (or insert size) between two paired RNA reads. Note that this can be negative if fragments overlap.

Read Duplication

read_duplication.py calculates how many alignment positions have a certain number of exact duplicates. Note - plot truncated at 500 occurrences and binned.

Junction Annotation

Junction annotation compares detected splice junctions to a reference gene model. An RNA read can be spliced 2 or more times, each time is called a splicing event.

Junction Saturation

Junction Saturation counts the number of known splicing junctions that are observed in each dataset. If sequencing depth is sufficient, all (annotated) splice junctions should be rediscovered, resulting in a curve that reaches a plateau. Missing low abundance splice junctions can affect downstream analysis.

Click a line to see the data side by side (as in the original RSeQC plot).

Infer experiment

Infer experiment counts the percentage of reads and read pairs that match the strandedness of overlapping transcripts. It can be used to infer whether RNA-seq library preps are stranded (sense or antisense).

Bam Stat

All numbers reported in millions.

Samtools

Samtools is a suite of programs for interacting with high-throughput sequencing data.

Percent Mapped

Alignment metrics from samtools stats; mapped vs. unmapped reads.

For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

Alignment metrics

This module parses the output from samtools stats. All numbers in millions.

Samtools Flagstat

This module parses the output from samtools flagstat. All numbers in millions.

Mapped reads per contig

The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.

STAR

STAR is an ultrafast universal RNA-seq aligner.

Alignment Scores

Cutadapt

Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

Filtered Reads

This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.

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

Trimmed Sequence Lengths

This plot shows the number of reads with certain lengths of adapter trimmed.

Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.

See the cutadapt documentation for more information on how these numbers are generated.

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

FastQC (trimmed)

FastQC (trimmed) This section of the report shows FastQC results after adapter trimming.

Sequence Counts

Sequence counts for each sample. Duplicate read counts are an estimate only.

This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

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

Sequence Quality Histograms

The mean quality value across each base position in the read.

To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

Taken from the FastQC help:

The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

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.

From the FastQC help:

The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

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.

To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

To see the data as a line plot, as in the original FastQC graph, click on a sample track.

From the FastQC help:

Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

Click a sample row to see a line plot for that dataset.

Rollover for sample name

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%T: -

%C: -

%A: -

%G: -

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General Statistics

General Statistics: Columns

STAR_SALMON DESeq2 PCA plot

STAR_SALMON DESeq2 sample similarity

DupRadar

Preseq

Complexity curve

RSeQC

Read Distribution

Inner Distance

Read Duplication

Junction Annotation

Junction Saturation

Infer experiment

Bam Stat

Samtools

Percent Mapped Help

Alignment metrics

Samtools Flagstat

Mapped reads per contig

STAR

Alignment Scores

Cutadapt

Filtered Reads

Trimmed Sequence Lengths Help

FastQC (trimmed)

Sequence Counts Help

Sequence Quality Histograms Help

Per Sequence Quality Scores Help

Per Base Sequence Content Help

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