MultiQC Report

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

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Report generated on 2024-10-21, 08:57 based on data in:

/projectnb/wax-dk/max/G236_Gonzalez092024_RNAseq/SAMPLES
/projectnb/wax-dk/max/G236_Gonzalez092024_RNAseq/Scripts/03_FASTQC
/projectnb/wax-dk/max/G236_Gonzalez092024_RNAseq/Scripts/06_CollectMetrics

General Statistics

Showing ⁴⁵⁹/₄₅₉ rows and ¹⁶/₂₃ columns.

Sample Name	M Reads	M Reads Mapped	% Assigned	M Assigned	% rRNA	% mRNA	Insert Size	Mean Insert Size	% Dups	# Variants	% Aligned	M Aligned	% Duplication	% > Q30	Mb Q30 bases	GC content	% PF	% Adapter	% Dups	% GC	Length	% Failed	M Seqs
10_DW_073024_N10_S10_R1_001													32.1%	96.6%	6296.5	49.0%	99.0%	8.0%	77.0%	48%	101 bp	18%	33.0
10_DW_073024_N10_S10_R2_001																			77.5%	49%	101 bp	18%	33.0
11_DW_073024_N11_S11_R1_001													34.1%	96.8%	7655.0	48.6%	99.0%	8.2%	77.3%	48%	101 bp	18%	40.0
11_DW_073024_N11_S11_R2_001																			78.7%	49%	101 bp	18%	40.0
12_DW_073024_N12_S12_R1_001													34.2%	96.8%	6349.3	48.2%	99.1%	8.2%	77.0%	47%	101 bp	18%	33.1
12_DW_073024_N12_S12_R2_001																			78.2%	48%	101 bp	18%	33.1
13_DW_073024_N13_S13_R1_001													35.8%	96.4%	7804.5	48.3%	98.9%	7.8%	78.6%	47%	101 bp	27%	41.0
13_DW_073024_N13_S13_R2_001																			79.0%	48%	101 bp	18%	41.0
14_DW_073024_N14_S14_R1_001													32.0%	96.7%	6387.6	48.5%	99.0%	7.3%	76.0%	48%	101 bp	18%	33.4
14_DW_073024_N14_S14_R2_001																			76.5%	48%	101 bp	18%	33.4
15_DW_073024_N16_S15_R1_001													28.5%	96.6%	6236.4	49.1%	99.1%	7.3%	72.7%	48%	101 bp	27%	32.6
15_DW_073024_N16_S15_R2_001																			73.4%	49%	101 bp	18%	32.6
16_DW_073024_N17_S16_R1_001													24.1%	96.6%	6558.7	49.9%	98.9%	6.8%	68.2%	49%	101 bp	18%	34.3
16_DW_073024_N17_S16_R2_001																			68.4%	50%	101 bp	18%	34.3
17_DW_073024_N18_S17_R1_001													31.3%	96.5%	8191.0	49.2%	98.9%	6.0%	76.4%	48%	101 bp	18%	42.8
17_DW_073024_N18_S17_R2_001																			77.1%	49%	101 bp	18%	42.8
18_DW_073024_N19_S18_R1_001													30.7%	96.6%	7114.0	49.1%	99.1%	4.7%	75.7%	48%	101 bp	18%	37.0
18_DW_073024_N19_S18_R2_001																			76.4%	49%	101 bp	18%	37.0
19_DW_073024_N21_S19_R1_001													29.5%	96.7%	6827.5	49.1%	98.9%	5.0%	73.8%	48%	101 bp	27%	35.6
19_DW_073024_N21_S19_R2_001																			74.6%	49%	101 bp	18%	35.6
1_DW_073024_N1_S1_R1_001													32.8%	96.7%	7083.8	48.5%	99.1%	5.9%	76.2%	48%	101 bp	27%	36.9
1_DW_073024_N1_S1_R2_001																			76.4%	48%	101 bp	18%	36.9
20_DW_073024_N22_S20_R1_001													32.5%	96.6%	7541.1	48.9%	99.0%	5.1%	77.2%	48%	101 bp	18%	39.3
20_DW_073024_N22_S20_R2_001																			78.1%	49%	101 bp	18%	39.3
21_DW_073024_N23_S21_R1_001													26.5%	96.5%	6000.4	49.3%	98.9%	5.7%	71.5%	48%	101 bp	18%	31.3
21_DW_073024_N23_S21_R2_001																			72.2%	49%	101 bp	18%	31.3
22_DW_073024_N24_S22_R1_001													30.9%	96.7%	7612.4	49.1%	99.0%	4.6%	75.6%	48%	101 bp	18%	39.6
22_DW_073024_N24_S22_R2_001																			77.0%	49%	101 bp	18%	39.6
23_DW_073024_N25_S23_R1_001													29.0%	96.5%	7331.8	49.6%	98.9%	4.5%	74.7%	49%	101 bp	18%	38.2
23_DW_073024_N25_S23_R2_001																			75.6%	50%	101 bp	18%	38.2
24_DW_073024_N26_S24_R1_001													32.3%	96.6%	6127.0	48.7%	99.1%	5.3%	76.0%	48%	101 bp	27%	31.9
24_DW_073024_N26_S24_R2_001																			77.2%	49%	101 bp	18%	31.9
25_DW_073024_N27_S25_R1_001													31.3%	96.7%	6266.5	48.8%	98.9%	5.8%	75.8%	48%	101 bp	18%	32.7
25_DW_073024_N27_S25_R2_001																			76.6%	49%	101 bp	18%	32.7
26_DW_073024_N28_S26_R1_001													32.9%	96.6%	6275.9	48.4%	98.9%	5.5%	75.9%	48%	101 bp	18%	32.7
26_DW_073024_N28_S26_R2_001																			76.6%	48%	101 bp	18%	32.7
27_DW_073024_N29_S27_R1_001													35.6%	96.7%	7095.5	48.5%	99.0%	6.4%	78.1%	48%	101 bp	18%	37.0
27_DW_073024_N29_S27_R2_001																			78.9%	48%	101 bp	18%	37.0
28_DW_073024_N30_S28_R1_001													33.8%	96.8%	6606.1	48.3%	99.0%	5.4%	76.9%	47%	101 bp	18%	34.4
28_DW_073024_N30_S28_R2_001																			77.7%	48%	101 bp	18%	34.4
29_DW_073024_N31_S29_R1_001													32.6%	96.5%	7202.9	49.1%	99.0%	5.9%	77.6%	48%	101 bp	18%	37.6
29_DW_073024_N31_S29_R2_001																			78.8%	49%	101 bp	18%	37.6
2_DW_073024_N2_S2_R1_001													30.5%	96.6%	6181.4	48.5%	98.9%	6.1%	74.6%	48%	101 bp	18%	32.3
2_DW_073024_N2_S2_R2_001																			75.3%	48%	101 bp	18%	32.3
30_DW_073024_N32_S30_R1_001													30.2%	96.7%	5707.2	49.3%	99.0%	8.3%	74.8%	49%	101 bp	27%	29.9
30_DW_073024_N32_S30_R2_001																			75.5%	49%	101 bp	18%	29.9
31_DW_073024_N33_S31_R1_001													33.3%	96.7%	6367.8	49.0%	99.0%	7.0%	77.3%	48%	101 bp	18%	33.2
31_DW_073024_N33_S31_R2_001																			78.5%	49%	101 bp	18%	33.2
32_DW_073024_N34_S32_R1_001													32.3%	96.6%	6043.8	49.1%	99.0%	7.5%	76.3%	48%	101 bp	18%	31.6
32_DW_073024_N34_S32_R2_001																			77.5%	49%	101 bp	18%	31.6
33_DW_073024_N35_S33_R1_001													30.7%	96.6%	5975.6	48.9%	99.0%	6.6%	75.2%	48%	101 bp	18%	31.2
33_DW_073024_N35_S33_R2_001																			75.9%	49%	101 bp	18%	31.2
34_DW_073024_N36_S34_R1_001													31.2%	96.5%	5880.7	49.2%	98.9%	6.8%	75.9%	48%	101 bp	18%	30.8
34_DW_073024_N36_S34_R2_001																			77.0%	49%	101 bp	18%	30.8
35_DW_073024_N37_S35_R1_001													31.6%	96.5%	6442.2	49.2%	99.1%	6.8%	76.1%	48%	101 bp	18%	33.6
35_DW_073024_N37_S35_R2_001																			76.6%	49%	101 bp	18%	33.6
36_DW_073024_N38_S36_R1_001													32.9%	96.7%	7226.8	49.1%	99.1%	6.3%	77.3%	48%	101 bp	18%	37.6
36_DW_073024_N38_S36_R2_001																			78.8%	49%	101 bp	18%	37.6
37_DW_073024_N39_S37_R1_001													30.0%	96.6%	5573.4	49.1%	99.0%	8.9%	74.7%	48%	101 bp	18%	29.2
37_DW_073024_N39_S37_R2_001																			75.7%	49%	101 bp	18%	29.2
38_DW_073024_N40_S38_R1_001													30.8%	96.6%	6623.2	49.4%	99.0%	9.8%	75.3%	49%	101 bp	18%	34.8
38_DW_073024_N40_S38_R2_001																			76.6%	49%	101 bp	18%	34.8
39_DW_073024_N41_S39_R1_001													30.0%	96.5%	6175.9	49.5%	98.9%	7.7%	75.4%	49%	101 bp	18%	32.4
39_DW_073024_N41_S39_R2_001																			76.1%	49%	101 bp	18%	32.4
3_DW_073024_N3_S3_R1_001													32.2%	96.7%	6126.3	48.3%	99.0%	6.7%	76.1%	47%	101 bp	18%	32.0
3_DW_073024_N3_S3_R2_001																			76.6%	48%	101 bp	18%	32.0
40_DW_073024_N42_S40_R1_001													30.7%	96.6%	7627.6	49.4%	99.1%	8.7%	75.5%	49%	101 bp	18%	39.9
40_DW_073024_N42_S40_R2_001																			77.1%	49%	101 bp	18%	39.9
41_DW_073024_N44_S41_R1_001													30.7%	96.7%	6685.8	49.3%	99.1%	7.4%	75.5%	48%	101 bp	18%	34.9
41_DW_073024_N44_S41_R2_001																			77.4%	49%	101 bp	18%	34.9
42_DW_073024_N45_S42_R1_001													29.0%	96.6%	5641.2	49.2%	99.0%	7.2%	73.4%	48%	101 bp	18%	29.5
42_DW_073024_N45_S42_R2_001																			74.5%	49%	101 bp	18%	29.5
43_DW_073024_N46_S43_R1_001													28.9%	96.6%	5325.0	49.2%	98.8%	6.9%	73.8%	48%	101 bp	18%	27.9
43_DW_073024_N46_S43_R2_001																			74.7%	49%	101 bp	18%	27.9
44_DW_073024_N47_S44_R1_001													28.0%	96.6%	6625.5	49.5%	99.0%	6.8%	73.7%	49%	101 bp	18%	34.6
44_DW_073024_N47_S44_R2_001																			74.6%	49%	101 bp	18%	34.6
45_DW_073024_N48_S45_R1_001													27.0%	96.7%	5811.2	49.4%	99.0%	6.8%	72.1%	49%	101 bp	18%	30.3
45_DW_073024_N48_S45_R2_001																			73.2%	49%	101 bp	18%	30.3
46_DW_073024_N49_S46_R1_001													28.9%	96.6%	5659.3	49.1%	99.0%	8.7%	73.3%	48%	101 bp	18%	29.6
46_DW_073024_N49_S46_R2_001																			74.3%	49%	101 bp	18%	29.6
47_DW_073024_N50_S47_R1_001													30.3%	96.5%	6880.7	49.3%	99.0%	7.6%	75.2%	48%	101 bp	18%	36.0
47_DW_073024_N50_S47_R2_001																			76.2%	49%	101 bp	18%	36.0
48_DW_073024_N51_S48_R1_001													28.8%	96.7%	6319.1	49.2%	99.1%	7.8%	73.5%	48%	101 bp	18%	33.0
48_DW_073024_N51_S48_R2_001																			75.2%	49%	101 bp	18%	33.0
49_DW_073024_N52_S49_R1_001													30.4%	96.6%	6274.9	49.0%	99.0%	6.8%	75.1%	48%	101 bp	18%	32.8
49_DW_073024_N52_S49_R2_001																			76.0%	49%	101 bp	18%	32.8
4_DW_073024_N4_S4_R1_001													35.4%	96.7%	6474.2	48.3%	99.0%	7.0%	77.8%	48%	101 bp	18%	33.7
4_DW_073024_N4_S4_R2_001																			78.7%	48%	101 bp	18%	33.7
50_DW_073024_N53_S50_R1_001													30.7%	96.7%	7014.9	49.1%	99.1%	6.1%	75.1%	48%	101 bp	18%	36.5
50_DW_073024_N53_S50_R2_001																			76.9%	49%	101 bp	18%	36.5
51_DW_073024_N54_S51_R1_001													29.8%	96.7%	6767.3	48.9%	99.0%	6.7%	74.8%	48%	101 bp	18%	35.3
51_DW_073024_N54_S51_R2_001																			75.6%	49%	101 bp	18%	35.3
52_DW_073024_N55_S52_R1_001													28.4%	96.6%	6257.0	49.3%	99.0%	6.9%	73.8%	49%	101 bp	18%	32.7
52_DW_073024_N55_S52_R2_001																			74.7%	49%	101 bp	18%	32.7
53_DW_073024_N57_S53_R1_001													28.2%	96.3%	6394.9	49.2%	98.8%	7.2%	73.6%	48%	101 bp	18%	33.6
53_DW_073024_N57_S53_R2_001																			74.1%	49%	101 bp	18%	33.6
54_DW_073024_N58_S54_R1_001													29.2%	96.7%	6268.9	49.2%	99.0%	7.5%	73.6%	48%	101 bp	18%	32.7
54_DW_073024_N58_S54_R2_001																			74.8%	49%	101 bp	18%	32.7
55_DW_073024_N59_S55_R1_001													29.4%	96.6%	6708.4	49.1%	99.0%	7.1%	74.5%	48%	101 bp	18%	35.0
55_DW_073024_N59_S55_R2_001																			75.3%	49%	101 bp	18%	35.0
56_DW_073024_N60_S56_R1_001													31.0%	96.6%	6700.1	49.1%	98.9%	6.7%	75.3%	48%	101 bp	18%	35.0
56_DW_073024_N60_S56_R2_001																			76.1%	49%	101 bp	18%	35.0
57_DW_073024_N61_S57_R1_001													30.1%	96.5%	6336.7	49.1%	98.9%	5.4%	74.6%	48%	101 bp	18%	33.1
57_DW_073024_N61_S57_R2_001																			75.3%	49%	101 bp	18%	33.1
5_DW_073024_N5_S5_R1_001													33.8%	96.6%	6659.4	48.3%	99.0%	5.5%	77.3%	47%	101 bp	18%	34.7
5_DW_073024_N5_S5_R2_001																			78.4%	48%	101 bp	18%	34.7
6_DW_073024_N6_S6_R1_001													33.9%	96.7%	6018.8	48.2%	99.2%	6.8%	76.1%	47%	101 bp	18%	31.3
6_DW_073024_N6_S6_R2_001																			77.4%	48%	101 bp	18%	31.3
7_DW_073024_N7_S7_R1_001													31.8%	96.6%	6125.5	48.6%	99.0%	8.5%	76.0%	48%	101 bp	18%	32.1
7_DW_073024_N7_S7_R2_001																			77.0%	49%	101 bp	18%	32.1
8_DW_073024_N8_S8_R1_001													34.9%	96.7%	6984.8	48.5%	99.0%	6.7%	78.0%	48%	101 bp	27%	36.4
8_DW_073024_N8_S8_R2_001																			78.7%	48%	101 bp	18%	36.4
9_DW_073024_N9_S9_R1_001													32.4%	96.7%	5978.6	48.9%	99.0%	9.8%	76.6%	48%	101 bp	18%	31.4
9_DW_073024_N9_S9_R2_001																			77.5%	49%	101 bp	18%	31.4
G236_N01_G236_N01											79.0%	29.2
G236_N01_primary_unique					1.6%	85.7%	260 bp	653 bp	36.2%
G236_N01_sorted			90.3%	26.3
G236_N01_statistics_for_all_accepted_reads	75.3	75.3
G236_N01_statistics_for_primary_reads	65.0	65.0
G236_N01_statistics_for_primary_unique_reads	58.3	58.3
G236_N02_G236_N02											81.0%	26.1
G236_N02_primary_unique					1.3%	86.1%	281 bp	708 bp	34.6%
G236_N02_sorted			90.5%	23.6
G236_N02_statistics_for_all_accepted_reads	66.5	66.5
G236_N02_statistics_for_primary_reads	58.0	58.0
G236_N02_statistics_for_primary_unique_reads	52.3	52.3
G236_N03_G236_N03											80.4%	25.7
G236_N03_primary_unique					1.2%	87.0%	287 bp	730 bp	36.4%
G236_N03_sorted			90.3%	23.2
G236_N03_statistics_for_all_accepted_reads	66.0	66.0
G236_N03_statistics_for_primary_reads	57.3	57.3
G236_N03_statistics_for_primary_unique_reads	51.4	51.4
G236_N04_G236_N04											80.3%	27.1
G236_N04_primary_unique					1.7%	87.2%	288 bp	739 bp	40.0%
G236_N04_sorted			89.9%	24.4
G236_N04_statistics_for_all_accepted_reads	70.1	70.1
G236_N04_statistics_for_primary_reads	60.7	60.7
G236_N04_statistics_for_primary_unique_reads	54.2	54.2
G236_N05_G236_N05											80.1%	27.8
G236_N05_primary_unique					1.4%	87.2%	306 bp	780 bp	37.8%
G236_N05_sorted			90.0%	25.0
G236_N05_statistics_for_all_accepted_reads	72.2	72.2
G236_N05_statistics_for_primary_reads	62.3	62.3
G236_N05_statistics_for_primary_unique_reads	55.6	55.6
G236_N06_G236_N06											79.3%	24.8
G236_N06_primary_unique					1.3%	87.1%	283 bp	724 bp	36.8%
G236_N06_sorted			90.5%	22.5
G236_N06_statistics_for_all_accepted_reads	65.0	65.0
G236_N06_statistics_for_primary_reads	55.7	55.7
G236_N06_statistics_for_primary_unique_reads	49.7	49.7
G236_N07_G236_N07											80.2%	25.8
G236_N07_primary_unique					1.8%	87.3%	286 bp	731 bp	36.3%
G236_N07_sorted			90.3%	23.3
G236_N07_statistics_for_all_accepted_reads	65.9	65.9
G236_N07_statistics_for_primary_reads	57.3	57.3
G236_N07_statistics_for_primary_unique_reads	51.5	51.5
G236_N08_G236_N08											75.0%	27.3
G236_N08_primary_unique					2.2%	87.1%	253 bp	646 bp	37.0%
G236_N08_sorted			90.2%	24.7
G236_N08_statistics_for_all_accepted_reads	73.4	73.4
G236_N08_statistics_for_primary_reads	61.7	61.7
G236_N08_statistics_for_primary_unique_reads	54.7	54.7
G236_N09_G236_N09											75.9%	23.8
G236_N09_primary_unique					2.6%	86.9%	258 bp	660 bp	36.1%
G236_N09_sorted			90.2%	21.5
G236_N09_statistics_for_all_accepted_reads	62.2	62.2
G236_N09_statistics_for_primary_reads	53.2	53.2
G236_N09_statistics_for_primary_unique_reads	47.6	47.6
G236_N10_G236_N10											78.5%	25.8
G236_N10_primary_unique					2.2%	87.6%	280 bp	729 bp	37.4%
G236_N10_sorted			90.6%	23.4
G236_N10_statistics_for_all_accepted_reads	66.0	66.0
G236_N10_statistics_for_primary_reads	57.4	57.4
G236_N10_statistics_for_primary_unique_reads	51.7	51.7
G236_N11_G236_N11											74.0%	29.6
G236_N11_primary_unique					2.0%	87.0%	250 bp	627 bp	36.6%
G236_N11_sorted			90.9%	26.9
G236_N11_statistics_for_all_accepted_reads	78.0	78.0
G236_N11_statistics_for_primary_reads	66.1	66.1
G236_N11_statistics_for_primary_unique_reads	59.2	59.2
G236_N12_G236_N12											71.1%	23.6
G236_N12_primary_unique					1.4%	87.7%	262 bp	663 bp	33.9%
G236_N12_sorted			90.9%	21.4
G236_N12_statistics_for_all_accepted_reads	64.6	64.6
G236_N12_statistics_for_primary_reads	53.5	53.5
G236_N12_statistics_for_primary_unique_reads	47.1	47.1
G236_N13_G236_N13											70.9%	29.0
G236_N13_primary_unique					2.0%	86.6%	251 bp	628 bp	37.2%
G236_N13_sorted			90.4%	26.2
G236_N13_statistics_for_all_accepted_reads	79.0	79.0
G236_N13_statistics_for_primary_reads	65.8	65.8
G236_N13_statistics_for_primary_unique_reads	58.0	58.0
G236_N14_G236_N14											76.6%	25.6
G236_N14_primary_unique					2.2%	86.5%	283 bp	715 bp	34.3%
G236_N14_sorted			90.4%	23.1
G236_N14_statistics_for_all_accepted_reads	67.1	67.1
G236_N14_statistics_for_primary_reads	57.2	57.2
G236_N14_statistics_for_primary_unique_reads	51.1	51.1
G236_N16_G236_N16											84.0%	27.4
G236_N16_primary_unique					2.0%	86.4%	249 bp	605 bp	34.1%
G236_N16_sorted			91.0%	24.9
G236_N16_statistics_for_all_accepted_reads	66.7	66.7
G236_N16_statistics_for_primary_reads	59.6	59.6
G236_N16_statistics_for_primary_unique_reads	54.8	54.8
G236_N17_G236_N17											85.0%	29.1
G236_N17_primary_unique					1.6%	88.0%	228 bp	526 bp	30.1%
G236_N17_sorted			92.6%	27.0
G236_N17_statistics_for_all_accepted_reads	69.0	69.0
G236_N17_statistics_for_primary_reads	62.6	62.6
G236_N17_statistics_for_primary_unique_reads	58.3	58.3
G236_N18_G236_N18											84.6%	36.2
G236_N18_primary_unique					1.3%	88.8%	263 bp	656 bp	38.7%
G236_N18_sorted			91.2%	33.0
G236_N18_statistics_for_all_accepted_reads	88.0	88.0
G236_N18_statistics_for_primary_reads	79.0	79.0
G236_N18_statistics_for_primary_unique_reads	72.4	72.4
G236_N19_G236_N19											84.8%	31.4
G236_N19_primary_unique					1.6%	88.3%	268 bp	666 bp	37.4%
G236_N19_sorted			91.0%	28.6
G236_N19_statistics_for_all_accepted_reads	76.2	76.2
G236_N19_statistics_for_primary_reads	68.5	68.5
G236_N19_statistics_for_primary_unique_reads	62.7	62.7
G236_N21_G236_N21											87.1%	31.0
G236_N21_primary_unique					1.1%	88.6%	271 bp	670 bp	36.3%
G236_N21_sorted			91.6%	28.3
G236_N21_statistics_for_all_accepted_reads	74.2	74.2
G236_N21_statistics_for_primary_reads	67.2	67.2
G236_N21_statistics_for_primary_unique_reads	61.9	61.9
G236_N22_G236_N22											83.1%	32.6
G236_N22_primary_unique					1.5%	88.1%	280 bp	701 bp	38.9%
G236_N22_sorted			90.8%	29.6
G236_N22_statistics_for_all_accepted_reads	80.9	80.9
G236_N22_statistics_for_primary_reads	71.7	71.7
G236_N22_statistics_for_primary_unique_reads	65.2	65.2
G236_N23_G236_N23											86.5%	27.1
G236_N23_primary_unique					1.3%	88.3%	257 bp	619 bp	32.8%
G236_N23_sorted			91.6%	24.8
G236_N23_statistics_for_all_accepted_reads	64.6	64.6
G236_N23_statistics_for_primary_reads	58.6	58.6
G236_N23_statistics_for_primary_unique_reads	54.1	54.1
G236_N24_G236_N24											85.5%	33.8
G236_N24_primary_unique					1.4%	88.8%	281 bp	701 bp	37.9%
G236_N24_sorted			91.3%	30.9
G236_N24_statistics_for_all_accepted_reads	81.7	81.7
G236_N24_statistics_for_primary_reads	73.6	73.6
G236_N24_statistics_for_primary_unique_reads	67.7	67.7
G236_N25_G236_N25											86.5%	33.1
G236_N25_primary_unique					1.8%	88.9%	274 bp	678 bp	36.5%
G236_N25_sorted			91.5%	30.3
G236_N25_statistics_for_all_accepted_reads	78.8	78.8
G236_N25_statistics_for_primary_reads	71.6	71.6
G236_N25_statistics_for_primary_unique_reads	66.2	66.2
G236_N26_G236_N26											80.8%	25.8
G236_N26_primary_unique					2.0%	87.8%	263 bp	653 bp	37.0%
G236_N26_sorted			90.3%	23.3
G236_N26_statistics_for_all_accepted_reads	65.7	65.7
G236_N26_statistics_for_primary_reads	57.3	57.3
G236_N26_statistics_for_primary_unique_reads	51.5	51.5
G236_N27_G236_N27											82.8%	27.0
G236_N27_primary_unique					1.3%	88.4%	271 bp	684 bp	37.1%
G236_N27_sorted			90.8%	24.6
G236_N27_statistics_for_all_accepted_reads	67.4	67.4
G236_N27_statistics_for_primary_reads	59.6	59.6
G236_N27_statistics_for_primary_unique_reads	54.1	54.1
G236_N28_G236_N28											77.3%	25.3
G236_N28_primary_unique					1.3%	87.7%	289 bp	732 bp	35.2%
G236_N28_sorted			91.0%	23.0
G236_N28_statistics_for_all_accepted_reads	65.8	65.8
G236_N28_statistics_for_primary_reads	56.5	56.5
G236_N28_statistics_for_primary_unique_reads	50.6	50.6
G236_N29_G236_N29											74.5%	27.6
G236_N29_primary_unique					3.3%	85.9%	258 bp	636 bp	37.6%
G236_N29_sorted			89.6%	24.7
G236_N29_statistics_for_all_accepted_reads	73.5	73.5
G236_N29_statistics_for_primary_reads	62.2	62.2
G236_N29_statistics_for_primary_unique_reads	55.2	55.2
G236_N30_G236_N30											74.8%	25.7
G236_N30_primary_unique					1.2%	87.8%	274 bp	684 bp	34.9%
G236_N30_sorted			91.0%	23.4
G236_N30_statistics_for_all_accepted_reads	68.2	68.2
G236_N30_statistics_for_primary_reads	57.8	57.8
G236_N30_statistics_for_primary_unique_reads	51.4	51.4
G236_N31_G236_N31											84.3%	31.7
G236_N31_primary_unique					1.4%	88.8%	371 bp	905 bp	39.8%
G236_N31_sorted			91.1%	28.8
G236_N31_statistics_for_all_accepted_reads	78.1	78.1
G236_N31_statistics_for_primary_reads	69.5	69.5
G236_N31_statistics_for_primary_unique_reads	63.4	63.4
G236_N32_G236_N32											83.2%	24.8
G236_N32_primary_unique					1.6%	88.5%	259 bp	678 bp	37.3%
G236_N32_sorted			91.2%	22.6
G236_N32_statistics_for_all_accepted_reads	60.9	60.9
G236_N32_statistics_for_primary_reads	54.4	54.4
G236_N32_statistics_for_primary_unique_reads	49.7	49.7
G236_N33_G236_N33											84.1%	28.0
G236_N33_primary_unique					1.8%	88.4%	340 bp	857 bp	40.1%
G236_N33_sorted			90.9%	25.4
G236_N33_statistics_for_all_accepted_reads	69.2	69.2
G236_N33_statistics_for_primary_reads	61.5	61.5
G236_N33_statistics_for_primary_unique_reads	55.9	55.9
G236_N34_G236_N34											83.8%	26.5
G236_N34_primary_unique					1.9%	88.2%	334 bp	841 bp	39.4%
G236_N34_sorted			90.9%	24.1
G236_N34_statistics_for_all_accepted_reads	65.3	65.3
G236_N34_statistics_for_primary_reads	58.1	58.1
G236_N34_statistics_for_primary_unique_reads	53.0	53.0
G236_N35_G236_N35											82.9%	25.9
G236_N35_primary_unique					1.0%	88.7%	335 bp	852 bp	36.8%
G236_N35_sorted			91.6%	23.7
G236_N35_statistics_for_all_accepted_reads	63.9	63.9
G236_N35_statistics_for_primary_reads	56.8	56.8
G236_N35_statistics_for_primary_unique_reads	51.8	51.8
G236_N36_G236_N36											82.8%	25.5
G236_N36_primary_unique					2.7%	87.8%	320 bp	825 bp	37.7%
G236_N36_sorted			90.8%	23.1
G236_N36_statistics_for_all_accepted_reads	63.1	63.1
G236_N36_statistics_for_primary_reads	56.0	56.0
G236_N36_statistics_for_primary_unique_reads	51.0	51.0
G236_N37_G236_N37											83.5%	28.1
G236_N37_primary_unique					1.3%	88.7%	326 bp	833 bp	38.6%
G236_N37_sorted			91.7%	25.8
G236_N37_statistics_for_all_accepted_reads	68.6	68.6
G236_N37_statistics_for_primary_reads	61.3	61.3
G236_N37_statistics_for_primary_unique_reads	56.2	56.2
G236_N38_G236_N38											83.0%	31.2
G236_N38_primary_unique					1.3%	89.5%	367 bp	903 bp	40.0%
G236_N38_sorted			92.0%	28.7
G236_N38_statistics_for_all_accepted_reads	76.9	76.9
G236_N38_statistics_for_primary_reads	68.4	68.4
G236_N38_statistics_for_primary_unique_reads	62.5	62.5
G236_N39_G236_N39											82.2%	24.0
G236_N39_primary_unique					1.7%	87.9%	297 bp	768 bp	36.4%
G236_N39_sorted			91.1%	21.9
G236_N39_statistics_for_all_accepted_reads	59.3	59.3
G236_N39_statistics_for_primary_reads	52.7	52.7
G236_N39_statistics_for_primary_unique_reads	48.0	48.0
G236_N40_G236_N40											83.5%	29.1
G236_N40_primary_unique					1.9%	88.6%	315 bp	808 bp	38.2%
G236_N40_sorted			91.5%	26.6
G236_N40_statistics_for_all_accepted_reads	70.7	70.7
G236_N40_statistics_for_primary_reads	63.3	63.3
G236_N40_statistics_for_primary_unique_reads	58.1	58.1
G236_N41_G236_N41											82.8%	26.8
G236_N41_primary_unique					2.6%	87.8%	305 bp	788 bp	37.2%
G236_N41_sorted			91.0%	24.4
G236_N41_statistics_for_all_accepted_reads	65.5	65.5
G236_N41_statistics_for_primary_reads	58.5	58.5
G236_N41_statistics_for_primary_unique_reads	53.6	53.6
G236_N42_G236_N42											84.3%	33.7
G236_N42_primary_unique					2.2%	88.0%	287 bp	748 bp	37.7%
G236_N42_sorted			91.5%	30.8
G236_N42_statistics_for_all_accepted_reads	81.4	81.4
G236_N42_statistics_for_primary_reads	73.2	73.2
G236_N42_statistics_for_primary_unique_reads	67.3	67.3
G236_N44_G236_N44											83.7%	29.2
G236_N44_primary_unique					1.7%	88.8%	280 bp	716 bp	38.1%
G236_N44_sorted			92.3%	27.0
G236_N44_statistics_for_all_accepted_reads	70.9	70.9
G236_N44_statistics_for_primary_reads	63.6	63.6
G236_N44_statistics_for_primary_unique_reads	58.4	58.4
G236_N45_G236_N45											85.1%	25.1
G236_N45_primary_unique					1.6%	88.7%	313 bp	807 bp	35.7%
G236_N45_sorted			92.0%	23.1
G236_N45_statistics_for_all_accepted_reads	60.1	60.1
G236_N45_statistics_for_primary_reads	54.4	54.4
G236_N45_statistics_for_primary_unique_reads	50.2	50.2
G236_N46_G236_N46											84.0%	23.4
G236_N46_primary_unique					1.5%	88.7%	317 bp	819 bp	35.6%
G236_N46_sorted			91.6%	21.4
G236_N46_statistics_for_all_accepted_reads	57.1	57.1
G236_N46_statistics_for_primary_reads	51.1	51.1
G236_N46_statistics_for_primary_unique_reads	46.8	46.8
G236_N47_G236_N47											84.8%	29.4
G236_N47_primary_unique					1.5%	88.9%	278 bp	712 bp	34.9%
G236_N47_sorted			92.0%	27.0
G236_N47_statistics_for_all_accepted_reads	70.4	70.4
G236_N47_statistics_for_primary_reads	63.6	63.6
G236_N47_statistics_for_primary_unique_reads	58.7	58.7
G236_N48_G236_N48											85.0%	25.8
G236_N48_primary_unique					1.4%	88.1%	261 bp	664 bp	33.3%
G236_N48_sorted			91.8%	23.7
G236_N48_statistics_for_all_accepted_reads	61.8	61.8
G236_N48_statistics_for_primary_reads	55.8	55.8
G236_N48_statistics_for_primary_unique_reads	51.5	51.5
G236_N49_G236_N49											84.8%	25.2
G236_N49_primary_unique					1.1%	88.4%	272 bp	693 bp	35.7%
G236_N49_sorted			91.6%	23.0
G236_N49_statistics_for_all_accepted_reads	60.8	60.8
G236_N49_statistics_for_primary_reads	54.7	54.7
G236_N49_statistics_for_primary_unique_reads	50.3	50.3
G236_N50_G236_N50											84.3%	30.3
G236_N50_primary_unique					1.6%	88.6%	284 bp	729 bp	37.4%
G236_N50_sorted			91.6%	27.8
G236_N50_statistics_for_all_accepted_reads	73.6	73.6
G236_N50_statistics_for_primary_reads	66.0	66.0
G236_N50_statistics_for_primary_unique_reads	60.7	60.7
G236_N51_G236_N51											84.5%	27.9
G236_N51_primary_unique					1.4%	87.9%	262 bp	662 bp	35.1%
G236_N51_sorted			91.2%	25.4
G236_N51_statistics_for_all_accepted_reads	67.9	67.9
G236_N51_statistics_for_primary_reads	60.8	60.8
G236_N51_statistics_for_primary_unique_reads	55.7	55.7
G236_N52_G236_N52											85.4%	28.0
G236_N52_primary_unique					1.1%	88.8%	276 bp	705 bp	37.4%
G236_N52_sorted			91.3%	25.5
G236_N52_statistics_for_all_accepted_reads	67.9	67.9
G236_N52_statistics_for_primary_reads	61.1	61.1
G236_N52_statistics_for_primary_unique_reads	56.0	56.0
G236_N53_G236_N53											85.4%	31.2
G236_N53_primary_unique					1.1%	88.8%	283 bp	725 bp	37.9%
G236_N53_sorted			91.6%	28.6
G236_N53_statistics_for_all_accepted_reads	75.7	75.7
G236_N53_statistics_for_primary_reads	68.1	68.1
G236_N53_statistics_for_primary_unique_reads	62.4	62.4
G236_N54_G236_N54											84.6%	29.9
G236_N54_primary_unique					0.8%	88.8%	288 bp	747 bp	36.4%
G236_N54_sorted			91.5%	27.3
G236_N54_statistics_for_all_accepted_reads	72.4	72.4
G236_N54_statistics_for_primary_reads	65.1	65.1
G236_N54_statistics_for_primary_unique_reads	59.7	59.7
G236_N55_G236_N55											84.9%	27.7
G236_N55_primary_unique					1.0%	89.4%	282 bp	733 bp	35.0%
G236_N55_sorted			92.3%	25.6
G236_N55_statistics_for_all_accepted_reads	66.5	66.5
G236_N55_statistics_for_primary_reads	60.1	60.1
G236_N55_statistics_for_primary_unique_reads	55.5	55.5
G236_N57_G236_N57											85.1%	28.5
G236_N57_primary_unique					1.1%	88.7%	285 bp	729 bp	34.6%
G236_N57_sorted			92.2%	26.3
G236_N57_statistics_for_all_accepted_reads	69.0	69.0
G236_N57_statistics_for_primary_reads	62.0	62.0
G236_N57_statistics_for_primary_unique_reads	57.1	57.1
G236_N58_G236_N58											85.6%	28.0
G236_N58_primary_unique					1.0%	89.2%	279 bp	715 bp	35.2%
G236_N58_sorted			92.4%	25.9
G236_N58_statistics_for_all_accepted_reads	67.9	67.9
G236_N58_statistics_for_primary_reads	60.8	60.8
G236_N58_statistics_for_primary_unique_reads	56.1	56.1
G236_N59_G236_N59											84.7%	29.7
G236_N59_primary_unique					1.4%	88.8%	289 bp	737 bp	35.2%
G236_N59_sorted			91.9%	27.3
G236_N59_statistics_for_all_accepted_reads	72.6	72.6
G236_N59_statistics_for_primary_reads	64.7	64.7
G236_N59_statistics_for_primary_unique_reads	59.4	59.4
G236_N60_G236_N60											84.7%	29.6
G236_N60_primary_unique					1.7%	88.4%	254 bp	618 bp	37.7%
G236_N60_sorted			92.2%	27.3
G236_N60_statistics_for_all_accepted_reads	72.6	72.6
G236_N60_statistics_for_primary_reads	64.7	64.7
G236_N60_statistics_for_primary_unique_reads	59.3	59.3
G236_N61_G236_N61											85.6%	28.3
G236_N61_primary_unique					1.0%	88.7%	304 bp	776 bp	37.0%
G236_N61_sorted			91.6%	25.9
G236_N61_statistics_for_all_accepted_reads	68.4	68.4
G236_N61_statistics_for_primary_reads	61.6	61.6
G236_N61_statistics_for_primary_unique_reads	56.7	56.7
multiqc										0
multiqc_general_stats										0
multiqc_sources										0

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
\|\|	featureCounts	% Assigned	% Assigned reads	`percent_assigned`	None
\|\|	featureCounts	M Assigned	Assigned reads (millions)	`Assigned`	read_count
\|\|	Picard	% rRNA	Percent of aligned bases overlapping ribosomal RNA regions	`PCT_RIBOSOMAL_BASES`	None
\|\|	Picard	% mRNA	Percent of aligned bases overlapping UTRs and coding regions of mRNA transcripts	`PCT_MRNA_BASES`	None
\|\|	Picard	Insert Size	Median Insert Size, all read orientations (bp)	`summed_median`	None
\|\|	Picard	Mean Insert Size	Mean Insert Size, all read orientations (bp)	`summed_mean`	None
\|\|	Picard	% Dups	Mark Duplicates - Percent Duplication	`PERCENT_DUPLICATION`	None
\|\|	Snippy	# Variants	Total variants detected.	`VariantTotal`	variant_count
\|\|	STAR	% Aligned	% Uniquely mapped reads	`uniquely_mapped_percent`	None
\|\|	STAR	M Aligned	Uniquely mapped reads (millions)	`uniquely_mapped`	read_count
\|\|	fastp	% Duplication	Duplication rate before filtering	`pct_duplication`	None
\|\|	fastp	% > Q30	Percentage of reads > Q30 after filtering	`after_filtering_q30_rate`	None
\|\|	fastp	Mb Q30 bases	Bases > Q30 after filtering (millions)	`after_filtering_q30_bases`	base_count
\|\|	fastp	GC content	GC content after filtering	`after_filtering_gc_content`	None
\|\|	fastp	% PF	Percent reads passing filter	`pct_surviving`	None
\|\|	fastp	% Adapter	Percentage adapter-trimmed reads	`pct_adapter`	None
\|\|	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

RSeQC

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

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).

featureCounts

Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

Picard

Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

Insert Size

Plot shows the number of reads at a given insert size. Reads with different orientations are summed.

Mark Duplicates

Number of reads, categorised by duplication state. Pair counts are doubled - see help text for details.

The table in the Picard metrics file contains some columns referring read pairs and some referring to single reads.

To make the numbers in this plot sum correctly, values referring to pairs are doubled according to the scheme below:

READS_IN_DUPLICATE_PAIRS = 2 * READ_PAIR_DUPLICATES
READS_IN_UNIQUE_PAIRS = 2 * (READ_PAIRS_EXAMINED - READ_PAIR_DUPLICATES)
READS_IN_UNIQUE_UNPAIRED = UNPAIRED_READS_EXAMINED - UNPAIRED_READ_DUPLICATES
READS_IN_DUPLICATE_PAIRS_OPTICAL = 2 * READ_PAIR_OPTICAL_DUPLICATES
READS_IN_DUPLICATE_PAIRS_NONOPTICAL = READS_IN_DUPLICATE_PAIRS - READS_IN_DUPLICATE_PAIRS_OPTICAL
READS_IN_DUPLICATE_UNPAIRED = UNPAIRED_READ_DUPLICATES
READS_UNMAPPED = UNMAPPED_READS

RnaSeqMetrics Assignment

Number of bases in primary alignments that align to regions in the reference genome.

RnaSeqMetrics Strand Mapping

Number of aligned reads that map to the correct strand.

Gene Coverage

Samtools

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

Samtools Flagstat

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

Snippy

Snippy is used for rapid haploid variant calling and core genome alignment.

Snippy Variants

This plot shows the different variant types reported by snippy.

Error - was not able to plot data.

STAR

STAR is an ultrafast universal RNA-seq aligner.

Alignment Scores

Gene Counts

Statistics from results generated using --quantMode GeneCounts. The three tabs show counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA and counts for the 2nd read strand aligned with RNA.

fastp

fastp An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...)

Filtered Reads

Filtering statistics of sampled reads.

Insert Sizes

Insert size estimation of sampled reads.

Sequence Quality

Average sequencing quality over each base of all reads.

GC Content

Average GC content over each base of all reads.

N content

Average N content over each base of all reads.

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.

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

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.

From the FastQC help:

This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

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

Per Base N Content

The percentage of base calls at each position for which an N was called.

From the FastQC help:

If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

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

Sequence Length Distribution

All samples have sequences of a single length (101bp).

Sequence Duplication Levels

The relative level of duplication found for every sequence.

From the FastQC Help:

In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

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.

In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

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

Overrepresented sequences

The total amount of overrepresented sequences found in each library.

FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

From the FastQC Help:

A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

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

Adapter Content

The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

Note that only samples with ≥ 0.1% adapter contamination are shown.

There may be several lines per sample, as one is shown for each adapter detected in the file.

From the FastQC Help:

The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

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

Status Checks

Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

Min:

Max:

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General Statistics

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RSeQC

Infer experiment

featureCounts

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Insert Size

Mark Duplicates Help

RnaSeqMetrics Assignment

RnaSeqMetrics Strand Mapping

Gene Coverage

Samtools

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Snippy

Snippy Variants

STAR

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fastp

Filtered Reads

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GC Content

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FastQC

Sequence Quality Histograms Help

Per Sequence Quality Scores Help

Per Base Sequence Content Help

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Per Sequence GC Content Help

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Sequence Length Distribution

Sequence Duplication Levels Help

Overrepresented sequences Help

Adapter Content Help

Status Checks Help

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Sequence Quality Histograms

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