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 2024-11-20, 09:08 based on data in:

/projectnb/wax-dk/max/G239/SAMPLES
/projectnb/wax-dk/max/G239/Scripts/03_FASTQC
/projectnb/wax-dk/max/G239/Scripts/06_CollectMetrics

General Statistics

Showing ³²⁰/₃₂₀ rows and ¹⁵/₂₂ columns.

Sample Name	M Reads	M Reads Mapped	% Assigned	M Assigned	% rRNA	% mRNA	Insert Size	Mean Insert Size	% Dups	% Aligned	M Aligned	% Duplication	% > Q30	Mb Q30 bases	GC content	% PF	% Adapter	% Dups	% GC	Length	% Failed	M Seqs
G239_M01_CKDL240037415-1A_22TFMNLT3_L7_1												34.1%	97.9%	9154.4	50.8%	99.4%	54.6%	76.5%	51%	150 bp	36%	35.5
G239_M01_CKDL240037415-1A_22TFMNLT3_L7_2																		76.5%	51%	150 bp	27%	35.5
G239_M01_G239_M01										63.9%	22.7
G239_M01_primary_unique					0.6%	88.0%	293 bp	738 bp	42.9%
G239_M01_sorted			93.4%	21.2
G239_M01_statistics_for_all_accepted_reads	56.7	56.7
G239_M01_statistics_for_primary_reads	49.1	49.1
G239_M01_statistics_for_primary_unique_reads	45.4	45.4
G239_M02_CKDL240037415-1A_22TFMNLT3_L7_1												30.2%	98.1%	4497.9	49.8%	99.5%	44.0%	70.8%	50%	150 bp	36%	16.8
G239_M02_CKDL240037415-1A_22TFMNLT3_L7_2																		70.5%	50%	150 bp	27%	16.8
G239_M02_G239_M02										67.7%	11.4
G239_M02_primary_unique					0.4%	85.7%	270 bp	656 bp	35.4%
G239_M02_sorted			92.5%	10.5
G239_M02_statistics_for_all_accepted_reads	28.6	28.6
G239_M02_statistics_for_primary_reads	24.7	24.7
G239_M02_statistics_for_primary_unique_reads	22.7	22.7
G239_M03_CKDL240037415-1A_22TFMNLT3_L7_1												30.1%	98.1%	4022.6	50.6%	99.4%	46.4%	72.3%	51%	150 bp	36%	15.2
G239_M03_CKDL240037415-1A_22TFMNLT3_L7_2																		71.9%	51%	150 bp	27%	15.2
G239_M03_G239_M03										65.0%	9.9
G239_M03_primary_unique					1.1%	89.0%	325 bp	798 bp	34.5%
G239_M03_sorted			94.0%	9.3
G239_M03_statistics_for_all_accepted_reads	24.7	24.7
G239_M03_statistics_for_primary_reads	21.3	21.3
G239_M03_statistics_for_primary_unique_reads	19.8	19.8
G239_M04_CKDL240037415-1A_22TFMNLT3_L7_1												28.5%	97.9%	4409.2	51.2%	99.5%	57.6%	71.4%	52%	150 bp	36%	17.4
G239_M04_CKDL240037415-1A_22TFMNLT3_L7_2																		71.3%	51%	150 bp	27%	17.4
G239_M04_G239_M04										60.7%	10.5
G239_M04_primary_unique					0.3%	89.8%	342 bp	821 bp	35.7%
G239_M04_sorted			94.4%	10.0
G239_M04_statistics_for_all_accepted_reads	26.6	26.6
G239_M04_statistics_for_primary_reads	22.8	22.8
G239_M04_statistics_for_primary_unique_reads	21.1	21.1
G239_M05_CKDL240037415-1A_22TFMNLT3_L7_1												30.0%	97.9%	5676.2	51.8%	99.5%	49.4%	74.1%	52%	150 bp	36%	21.7
G239_M05_CKDL240037415-1A_22TFMNLT3_L7_2																		75.1%	52%	150 bp	27%	21.7
G239_M05_G239_M05										66.9%	14.5
G239_M05_primary_unique					0.5%	92.0%	438 bp	941 bp	38.8%
G239_M05_sorted			95.5%	13.9
G239_M05_statistics_for_all_accepted_reads	36.3	36.3
G239_M05_statistics_for_primary_reads	31.3	31.3
G239_M05_statistics_for_primary_unique_reads	29.1	29.1
G239_M06_CKDL240037415-1A_22TFMNLT3_L7_1												34.7%	97.9%	8925.0	50.9%	99.1%	56.3%	77.0%	51%	150 bp	36%	34.9
G239_M06_CKDL240037415-1A_22TFMNLT3_L7_2																		76.8%	51%	150 bp	27%	34.9
G239_M06_G239_M06										61.2%	21.4
G239_M06_primary_unique					0.2%	87.9%	272 bp	676 bp	42.8%
G239_M06_sorted			93.7%	20.0
G239_M06_statistics_for_all_accepted_reads	55.0	55.0
G239_M06_statistics_for_primary_reads	46.6	46.6
G239_M06_statistics_for_primary_unique_reads	42.7	42.7
G239_M07_CKDL240037415-1A_22TFMNLT3_L7_1												29.7%	98.1%	4643.0	50.3%	99.5%	51.2%	71.4%	50%	150 bp	36%	17.7
G239_M07_CKDL240037415-1A_22TFMNLT3_L7_2																		71.0%	50%	150 bp	27%	17.7
G239_M07_G239_M07										64.9%	11.5
G239_M07_primary_unique					0.3%	86.7%	254 bp	629 bp	35.5%
G239_M07_sorted			93.2%	10.7
G239_M07_statistics_for_all_accepted_reads	28.8	28.8
G239_M07_statistics_for_primary_reads	24.9	24.9
G239_M07_statistics_for_primary_unique_reads	23.0	23.0
G239_M08_CKDL240037415-1A_22TFMNLT3_L7_1												33.8%	98.0%	6782.2	49.8%	99.4%	47.5%	75.0%	50%	150 bp	36%	25.7
G239_M08_CKDL240037415-1A_22TFMNLT3_L7_2																		74.7%	50%	150 bp	27%	25.7
G239_M08_G239_M08										64.9%	16.7
G239_M08_primary_unique					0.2%	86.5%	287 bp	714 bp	40.6%
G239_M08_sorted			92.8%	15.5
G239_M08_statistics_for_all_accepted_reads	42.1	42.1
G239_M08_statistics_for_primary_reads	36.3	36.3
G239_M08_statistics_for_primary_unique_reads	33.4	33.4
G239_M09_CKDL240037415-1A_22TFMNLT3_L7_1												28.2%	97.9%	6003.4	50.9%	99.5%	56.4%	71.4%	51%	150 bp	36%	23.6
G239_M09_CKDL240037415-1A_22TFMNLT3_L7_2																		72.2%	51%	150 bp	27%	23.6
G239_M09_G239_M09										61.8%	14.6
G239_M09_primary_unique					0.3%	87.0%	272 bp	678 bp	37.6%
G239_M09_sorted			93.4%	13.6
G239_M09_statistics_for_all_accepted_reads	36.0	36.0
G239_M09_statistics_for_primary_reads	31.4	31.4
G239_M09_statistics_for_primary_unique_reads	29.2	29.2
G239_M10_CKDL240037415-1A_22TFMNLT3_L7_1												32.8%	97.8%	8272.8	50.6%	99.5%	53.4%	75.6%	51%	150 bp	36%	32.1
G239_M10_CKDL240037415-1A_22TFMNLT3_L7_2																		76.0%	51%	150 bp	27%	32.1
G239_M10_G239_M10										61.5%	19.8
G239_M10_primary_unique					0.4%	87.5%	303 bp	750 bp	40.7%
G239_M10_sorted			93.6%	18.5
G239_M10_statistics_for_all_accepted_reads	49.9	49.9
G239_M10_statistics_for_primary_reads	42.9	42.9
G239_M10_statistics_for_primary_unique_reads	39.5	39.5
G239_M11_CKDL240037415-1A_22TFMNLT3_L7_1												36.3%	98.0%	11627.9	50.4%	99.1%	49.7%	78.2%	51%	150 bp	36%	44.5
G239_M11_CKDL240037415-1A_22TFMNLT3_L7_2																		77.7%	51%	150 bp	27%	44.5
G239_M11_G239_M11										65.3%	29.0
G239_M11_primary_unique					0.6%	88.1%	280 bp	680 bp	43.8%
G239_M11_sorted			93.5%	27.2
G239_M11_statistics_for_all_accepted_reads	72.4	72.4
G239_M11_statistics_for_primary_reads	62.8	62.8
G239_M11_statistics_for_primary_unique_reads	58.1	58.1
G239_M12_CKDL240037415-1A_22TFMNLT3_L7_1												32.9%	98.1%	5033.0	51.5%	99.5%	46.2%	75.7%	51%	150 bp	36%	19.0
G239_M12_CKDL240037415-1A_22TFMNLT3_L7_2																		76.5%	52%	150 bp	27%	19.0
G239_M12_G239_M12										71.6%	13.6
G239_M12_primary_unique					0.3%	92.6%	460 bp	935 bp	42.9%
G239_M12_sorted			94.9%	12.9
G239_M12_statistics_for_all_accepted_reads	33.0	33.0
G239_M12_statistics_for_primary_reads	29.1	29.1
G239_M12_statistics_for_primary_unique_reads	27.1	27.1
G239_M13_CKDL240037415-1A_22TFMNLT3_L7_1												28.8%	98.1%	4045.9	50.5%	99.4%	43.0%	70.2%	50%	150 bp	36%	15.2
G239_M13_CKDL240037415-1A_22TFMNLT3_L7_2																		69.8%	51%	150 bp	27%	15.2
G239_M13_G239_M13										68.8%	10.4
G239_M13_primary_unique					0.3%	89.5%	380 bp	883 bp	34.2%
G239_M13_sorted			94.8%	9.9
G239_M13_statistics_for_all_accepted_reads	25.5	25.5
G239_M13_statistics_for_primary_reads	22.4	22.4
G239_M13_statistics_for_primary_unique_reads	20.8	20.8
G239_M14_CKDL240037415-1A_22TFMNLT3_L7_1												28.0%	97.8%	4867.1	51.0%	99.5%	53.1%	69.8%	51%	150 bp	36%	19.0
G239_M14_CKDL240037415-1A_22TFMNLT3_L7_2																		70.8%	51%	150 bp	27%	19.0
G239_M14_G239_M14										62.6%	11.9
G239_M14_primary_unique					0.3%	88.2%	322 bp	755 bp	37.2%
G239_M14_sorted			94.4%	11.2
G239_M14_statistics_for_all_accepted_reads	28.8	28.8
G239_M14_statistics_for_primary_reads	25.4	25.4
G239_M14_statistics_for_primary_unique_reads	23.8	23.8
G239_M15_CKDL240037415-1A_22TFMNLT3_L7_1												33.3%	97.9%	5478.1	51.6%	99.5%	49.4%	77.4%	52%	150 bp	36%	21.0
G239_M15_CKDL240037415-1A_22TFMNLT3_L7_2																		78.6%	52%	150 bp	27%	21.0
G239_M15_G239_M15										66.8%	14.0
G239_M15_primary_unique					0.4%	92.6%	468 bp	932 bp	43.4%
G239_M15_sorted			94.7%	13.3
G239_M15_statistics_for_all_accepted_reads	35.2	35.2
G239_M15_statistics_for_primary_reads	30.3	30.3
G239_M15_statistics_for_primary_unique_reads	28.0	28.0
G239_M16_CKDL240037415-1A_22TFMNLT3_L7_1												32.9%	98.0%	9715.8	50.5%	99.4%	57.5%	77.2%	51%	150 bp	36%	38.2
G239_M16_CKDL240037415-1A_22TFMNLT3_L7_2																		77.2%	51%	150 bp	27%	38.2
G239_M16_G239_M16										62.5%	23.9
G239_M16_primary_unique					0.3%	88.7%	264 bp	648 bp	44.4%
G239_M16_sorted			94.0%	22.5
G239_M16_statistics_for_all_accepted_reads	58.9	58.9
G239_M16_statistics_for_primary_reads	51.5	51.5
G239_M16_statistics_for_primary_unique_reads	47.8	47.8
G239_M17_CKDL240037415-1A_22TFMNLT3_L7_1												30.4%	98.1%	5153.2	50.7%	99.5%	48.1%	73.3%	51%	150 bp	36%	19.5
G239_M17_CKDL240037415-1A_22TFMNLT3_L7_2																		73.3%	51%	150 bp	27%	19.5
G239_M17_G239_M17										68.4%	13.4
G239_M17_primary_unique					0.3%	90.0%	305 bp	745 bp	38.6%
G239_M17_sorted			94.6%	12.6
G239_M17_statistics_for_all_accepted_reads	32.3	32.3
G239_M17_statistics_for_primary_reads	28.6	28.6
G239_M17_statistics_for_primary_unique_reads	26.7	26.7
G239_M18_CKDL240037415-1A_22TFMNLT3_L7_1												34.3%	98.1%	3772.8	49.5%	99.3%	42.2%	75.0%	50%	150 bp	36%	14.1
G239_M18_CKDL240037415-1A_22TFMNLT3_L7_2																		74.7%	50%	150 bp	27%	14.1
G239_M18_G239_M18										60.0%	8.5
G239_M18_primary_unique					0.3%	90.1%	383 bp	892 bp	35.2%
G239_M18_sorted			93.5%	7.9
G239_M18_statistics_for_all_accepted_reads	22.5	22.5
G239_M18_statistics_for_primary_reads	18.7	18.7
G239_M18_statistics_for_primary_unique_reads	17.0	17.0
G239_M19_CKDL240037415-1A_22TFMNLT3_L7_1												25.6%	97.7%	4946.8	50.7%	99.3%	53.1%	69.1%	51%	150 bp	36%	19.3
G239_M19_CKDL240037415-1A_22TFMNLT3_L7_2																		69.8%	51%	150 bp	27%	19.3
G239_M19_G239_M19										61.1%	11.8
G239_M19_primary_unique					0.4%	87.8%	280 bp	701 bp	32.9%
G239_M19_sorted			94.2%	11.1
G239_M19_statistics_for_all_accepted_reads	29.4	29.4
G239_M19_statistics_for_primary_reads	25.4	25.4
G239_M19_statistics_for_primary_unique_reads	23.6	23.6
G239_M20_CKDL240037415-1A_22TFMNLT3_L7_1												27.0%	97.9%	5469.3	50.8%	99.5%	54.2%	70.9%	51%	150 bp	36%	21.3
G239_M20_CKDL240037415-1A_22TFMNLT3_L7_2																		71.5%	51%	150 bp	27%	21.3
G239_M20_G239_M20										62.0%	13.2
G239_M20_primary_unique					0.2%	88.4%	320 bp	809 bp	35.0%
G239_M20_sorted			94.6%	12.5
G239_M20_statistics_for_all_accepted_reads	32.8	32.8
G239_M20_statistics_for_primary_reads	28.5	28.5
G239_M20_statistics_for_primary_unique_reads	26.5	26.5
G239_M21_CKDL240037415-1A_22TFMNLT3_L7_1												32.7%	98.0%	8328.3	50.5%	99.4%	50.1%	75.6%	51%	150 bp	36%	31.8
G239_M21_CKDL240037415-1A_22TFMNLT3_L7_2																		75.6%	51%	150 bp	27%	31.8
G239_M21_G239_M21										70.1%	22.3
G239_M21_primary_unique					0.2%	88.0%	268 bp	648 bp	43.1%
G239_M21_sorted			93.6%	20.9
G239_M21_statistics_for_all_accepted_reads	52.8	52.8
G239_M21_statistics_for_primary_reads	47.7	47.7
G239_M21_statistics_for_primary_unique_reads	44.6	44.6
G239_M22_CKDL240037415-1A_22TFMNLT3_L7_1												33.3%	98.1%	9072.9	50.3%	99.5%	44.7%	75.2%	50%	150 bp	36%	33.9
G239_M22_CKDL240037415-1A_22TFMNLT3_L7_2																		75.3%	50%	150 bp	27%	33.9
G239_M22_G239_M22										73.3%	24.9
G239_M22_primary_unique					0.3%	86.3%	258 bp	613 bp	43.2%
G239_M22_sorted			93.2%	23.2
G239_M22_statistics_for_all_accepted_reads	57.9	57.9
G239_M22_statistics_for_primary_reads	52.9	52.9
G239_M22_statistics_for_primary_unique_reads	49.8	49.8
G239_M23_CKDL240037415-1A_22TFMNLT3_L7_1												32.8%	98.1%	6790.7	50.1%	99.4%	49.2%	74.4%	50%	150 bp	36%	25.9
G239_M23_CKDL240037415-1A_22TFMNLT3_L7_2																		73.5%	50%	150 bp	27%	25.9
G239_M23_G239_M23										69.2%	17.9
G239_M23_primary_unique					0.2%	86.4%	286 bp	727 bp	42.0%
G239_M23_sorted			93.0%	16.7
G239_M23_statistics_for_all_accepted_reads	43.5	43.5
G239_M23_statistics_for_primary_reads	38.6	38.6
G239_M23_statistics_for_primary_unique_reads	35.8	35.8
G239_M24_CKDL240037415-1A_22TFMNLT3_L7_1												28.3%	97.8%	6064.8	51.1%	99.5%	55.1%	71.3%	51%	150 bp	36%	23.7
G239_M24_CKDL240037415-1A_22TFMNLT3_L7_2																		72.1%	51%	150 bp	27%	23.7
G239_M24_G239_M24										66.0%	15.6
G239_M24_primary_unique					0.4%	88.2%	356 bp	824 bp	39.9%
G239_M24_sorted			94.3%	14.8
G239_M24_statistics_for_all_accepted_reads	37.2	37.2
G239_M24_statistics_for_primary_reads	33.3	33.3
G239_M24_statistics_for_primary_unique_reads	31.3	31.3
G239_M25_CKDL240037415-1A_22TFMNLT3_L7_1												27.2%	97.8%	5724.9	51.3%	99.4%	58.5%	71.6%	51%	150 bp	36%	22.7
G239_M25_CKDL240037415-1A_22TFMNLT3_L7_2																		71.4%	51%	150 bp	27%	22.7
G239_M25_G239_M25										63.9%	14.5
G239_M25_primary_unique					0.2%	88.5%	324 bp	785 bp	39.4%
G239_M25_sorted			94.5%	13.7
G239_M25_statistics_for_all_accepted_reads	34.3	34.3
G239_M25_statistics_for_primary_reads	30.9	30.9
G239_M25_statistics_for_primary_unique_reads	29.0	29.0
G239_M26_CKDL240037415-1A_22TFMNLT3_L7_1												35.2%	98.0%	10486.6	51.2%	99.4%	55.2%	77.0%	51%	150 bp	36%	40.5
G239_M26_CKDL240037415-1A_22TFMNLT3_L7_2																		76.6%	51%	150 bp	27%	40.5
G239_M26_G239_M26										68.6%	27.8
G239_M26_primary_unique					0.2%	89.2%	354 bp	808 bp	46.7%
G239_M26_sorted			94.8%	26.4
G239_M26_statistics_for_all_accepted_reads	66.5	66.5
G239_M26_statistics_for_primary_reads	59.2	59.2
G239_M26_statistics_for_primary_unique_reads	55.6	55.6
G239_M27_CKDL240037415-1A_22TFMNLT3_L7_1												29.2%	98.0%	5007.5	50.8%	99.4%	47.9%	70.8%	51%	150 bp	36%	18.9
G239_M27_CKDL240037415-1A_22TFMNLT3_L7_2																		70.7%	51%	150 bp	27%	18.9
G239_M27_G239_M27										72.4%	13.7
G239_M27_primary_unique					0.2%	88.3%	301 bp	738 bp	39.1%
G239_M27_sorted			94.5%	12.9
G239_M27_statistics_for_all_accepted_reads	32.2	32.2
G239_M27_statistics_for_primary_reads	29.1	29.1
G239_M27_statistics_for_primary_unique_reads	27.4	27.4
G239_M28_CKDL240037415-1A_22TFMNLT3_L7_1												33.4%	98.0%	8780.8	51.0%	99.4%	42.8%	76.3%	51%	150 bp	36%	32.9
G239_M28_CKDL240037415-1A_22TFMNLT3_L7_2																		75.7%	51%	150 bp	27%	32.9
G239_M28_G239_M28										74.2%	24.4
G239_M28_primary_unique					0.2%	89.9%	366 bp	847 bp	43.7%
G239_M28_sorted			94.9%	23.1
G239_M28_statistics_for_all_accepted_reads	56.9	56.9
G239_M28_statistics_for_primary_reads	51.7	51.7
G239_M28_statistics_for_primary_unique_reads	48.8	48.8
G239_M29_CKDL240037415-1A_22TFMNLT3_L7_1												27.9%	97.8%	7346.9	51.4%	99.3%	54.4%	71.6%	52%	150 bp	36%	28.7
G239_M29_CKDL240037415-1A_22TFMNLT3_L7_2																		72.2%	51%	150 bp	27%	28.7
G239_M29_G239_M29										66.8%	19.2
G239_M29_primary_unique					0.4%	88.5%	340 bp	806 bp	39.6%
G239_M29_sorted			94.8%	18.2
G239_M29_statistics_for_all_accepted_reads	44.3	44.3
G239_M29_statistics_for_primary_reads	40.5	40.5
G239_M29_statistics_for_primary_unique_reads	38.4	38.4
G239_M30_CKDL240037415-1A_22TFMNLT3_L7_1												30.2%	97.8%	6034.8	51.2%	99.4%	56.5%	72.7%	51%	150 bp	36%	23.7
G239_M30_CKDL240037415-1A_22TFMNLT3_L7_2																		72.5%	51%	150 bp	27%	23.7
G239_M30_G239_M30										65.5%	15.6
G239_M30_primary_unique					0.2%	88.3%	332 bp	790 bp	41.8%
G239_M30_sorted			94.3%	14.7
G239_M30_statistics_for_all_accepted_reads	36.8	36.8
G239_M30_statistics_for_primary_reads	33.1	33.1
G239_M30_statistics_for_primary_unique_reads	31.1	31.1
G239_M31_CKDL240037415-1A_22TFMNLT3_L7_1												33.8%	97.9%	7531.5	51.8%	99.3%	56.4%	76.8%	52%	150 bp	36%	29.4
G239_M31_CKDL240037415-1A_22TFMNLT3_L7_2																		76.4%	52%	150 bp	27%	29.4
G239_M31_G239_M31										68.6%	20.2
G239_M31_primary_unique					0.2%	91.7%	399 bp	843 bp	46.8%
G239_M31_sorted			95.5%	19.3
G239_M31_statistics_for_all_accepted_reads	46.7	46.7
G239_M31_statistics_for_primary_reads	42.5	42.5
G239_M31_statistics_for_primary_unique_reads	40.3	40.3
G239_M32_CKDL240037415-1A_22TFMNLT3_L7_1												32.6%	98.1%	3678.8	52.5%	99.4%	32.4%	74.8%	52%	150 bp	36%	13.4
G239_M32_CKDL240037415-1A_22TFMNLT3_L7_2																		75.7%	53%	150 bp	27%	13.4
G239_M32_G239_M32										81.8%	10.9
G239_M32_primary_unique					0.3%	95.4%	619 bp	1133 bp	42.4%
G239_M32_sorted			97.2%	10.6
G239_M32_statistics_for_all_accepted_reads	24.8	24.8
G239_M32_statistics_for_primary_reads	22.9	22.9
G239_M32_statistics_for_primary_unique_reads	21.9	21.9
G239_M33_CKDL240037415-1A_22TFMNLT3_L7_1												31.2%	98.0%	8370.7	50.8%	99.4%	45.9%	73.2%	51%	150 bp	36%	31.6
G239_M33_CKDL240037415-1A_22TFMNLT3_L7_2																		71.9%	51%	150 bp	27%	31.6
G239_M33_G239_M33										73.6%	23.2
G239_M33_primary_unique					0.3%	87.7%	328 bp	792 bp	41.3%
G239_M33_sorted			94.4%	21.9
G239_M33_statistics_for_all_accepted_reads	53.2	53.2
G239_M33_statistics_for_primary_reads	49.0	49.0
G239_M33_statistics_for_primary_unique_reads	46.5	46.5
G239_M34_CKDL240037415-1A_22TFMNLT3_L7_1												26.8%	97.8%	6963.8	51.2%	99.3%	53.7%	70.8%	51%	150 bp	36%	27.2
G239_M34_CKDL240037415-1A_22TFMNLT3_L7_2																		71.7%	51%	150 bp	27%	27.2
G239_M34_G239_M34										67.0%	18.2
G239_M34_primary_unique					0.5%	87.9%	326 bp	776 bp	39.4%
G239_M34_sorted			94.2%	17.2
G239_M34_statistics_for_all_accepted_reads	42.0	42.0
G239_M34_statistics_for_primary_reads	38.5	38.5
G239_M34_statistics_for_primary_unique_reads	36.5	36.5
G239_M35_CKDL240037415-1A_22TFMNLT3_L7_1												29.8%	97.8%	8470.2	51.4%	99.5%	57.1%	74.4%	52%	150 bp	36%	33.4
G239_M35_CKDL240037415-1A_22TFMNLT3_L7_2																		74.2%	51%	150 bp	27%	33.4
G239_M35_G239_M35										65.5%	21.9
G239_M35_primary_unique					0.2%	88.3%	314 bp	757 bp	41.2%
G239_M35_sorted			94.2%	20.6
G239_M35_statistics_for_all_accepted_reads	50.9	50.9
G239_M35_statistics_for_primary_reads	46.3	46.3
G239_M35_statistics_for_primary_unique_reads	43.7	43.7
G239_M36_CKDL240037415-1A_22TFMNLT3_L7_1												32.4%	98.0%	10622.0	51.3%	99.3%	59.4%	76.9%	52%	150 bp	36%	42.2
G239_M36_CKDL240037415-1A_22TFMNLT3_L7_2																		76.0%	51%	150 bp	27%	42.2
G239_M36_G239_M36										64.4%	27.2
G239_M36_primary_unique					0.2%	89.3%	291 bp	715 bp	44.5%
G239_M36_sorted			94.8%	25.8
G239_M36_statistics_for_all_accepted_reads	64.1	64.1
G239_M36_statistics_for_primary_reads	57.7	57.7
G239_M36_statistics_for_primary_unique_reads	54.3	54.3
G239_M37_CKDL240037415-1A_22TFMNLT3_L7_1												28.8%	98.1%	4208.8	51.5%	99.5%	40.3%	70.9%	51%	150 bp	36%	15.6
G239_M37_CKDL240037415-1A_22TFMNLT3_L7_2																		70.8%	52%	150 bp	27%	15.6
G239_M37_G239_M37										77.4%	12.0
G239_M37_primary_unique					0.3%	91.9%	448 bp	960 bp	37.7%
G239_M37_sorted			95.4%	11.5
G239_M37_statistics_for_all_accepted_reads	27.6	27.6
G239_M37_statistics_for_primary_reads	25.4	25.4
G239_M37_statistics_for_primary_unique_reads	24.1	24.1
G239_M38_CKDL240037415-1A_22TFMNLT3_L7_1												29.2%	98.0%	5372.6	51.4%	99.4%	45.9%	73.0%	51%	150 bp	36%	20.3
G239_M38_CKDL240037415-1A_22TFMNLT3_L7_2																		72.2%	51%	150 bp	27%	20.3
G239_M38_G239_M38										73.1%	14.9
G239_M38_primary_unique					0.2%	91.5%	379 bp	861 bp	38.8%
G239_M38_sorted			95.4%	14.2
G239_M38_statistics_for_all_accepted_reads	34.1	34.1
G239_M38_statistics_for_primary_reads	31.3	31.3
G239_M38_statistics_for_primary_unique_reads	29.7	29.7
G239_M39_CKDL240037415-1A_22TFMNLT3_L7_1												24.1%	97.8%	5024.1	51.1%	99.5%	59.3%	68.9%	52%	150 bp	36%	20.1
G239_M39_CKDL240037415-1A_22TFMNLT3_L7_2																		69.2%	51%	150 bp	27%	20.1
G239_M39_G239_M39										62.0%	12.4
G239_M39_primary_unique					0.3%	88.1%	291 bp	733 bp	35.6%
G239_M39_sorted			94.6%	11.8
G239_M39_statistics_for_all_accepted_reads	29.2	29.2
G239_M39_statistics_for_primary_reads	26.4	26.4
G239_M39_statistics_for_primary_unique_reads	24.9	24.9
G239_M40_CKDL240037415-1A_22TFMNLT3_L7_1												24.7%	97.6%	4348.6	51.8%	99.4%	61.9%	69.9%	52%	150 bp	36%	17.6
G239_M40_CKDL240037415-1A_22TFMNLT3_L7_2																		69.2%	52%	150 bp	27%	17.6
G239_M40_G239_M40										60.9%	10.7
G239_M40_primary_unique					0.5%	89.3%	298 bp	739 bp	35.7%
G239_M40_sorted			94.3%	10.1
G239_M40_statistics_for_all_accepted_reads	25.2	25.2
G239_M40_statistics_for_primary_reads	22.8	22.8
G239_M40_statistics_for_primary_unique_reads	21.5	21.5

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
\|\|	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.

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.

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.

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.

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.

Sequence Length Distribution

All samples have sequences of a single length (150bp).

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.

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.

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

General Statistics: Columns

RSeQC

Infer experiment

featureCounts

Picard

Insert Size

Mark Duplicates Help

RnaSeqMetrics Assignment

RnaSeqMetrics Strand Mapping

Gene Coverage

Samtools

Samtools Flagstat

STAR

Alignment Scores

Gene Counts

fastp

Filtered Reads

Insert Sizes

Sequence Quality

GC Content

N content

FastQC

Sequence Quality Histograms Help

Per Sequence Quality Scores Help

Per Base Sequence Content Help

Rollover for sample name

Per Sequence GC Content Help

Per Base N Content Help

Sequence Length Distribution

Sequence Duplication Levels Help

Overrepresented sequences Help

Adapter Content Help

Status Checks Help

v1.11

Highlight Samples

Rename Samples

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Mark Duplicates

Sequence Quality Histograms

Per Sequence Quality Scores

Per Base Sequence Content

Per Sequence GC Content

Per Base N Content

Sequence Duplication Levels

Overrepresented sequences

Adapter Content

Status Checks