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 2024-05-03, 14:58 based on data in: /scratch/7034305.1.linga/nxf.Q7noJH7yS5

General Statistics

Showing ²⁹⁰/₂₉₀ rows and ¹⁵/₂₀ columns.

Sample Name	M Reads	M Reads Mapped	Fragment Length	Number of Peaks	% Aligned	Insert Size	Mean Insert Size	Error rate	M Non-Primary	M Reads Mapped	% Mapped	% Proper Pairs	% MapQ 0 Reads	M Total seqs	% Aligned	% Dups	% GC	Read Length	% Failed	M Seqs
G222_M09															93.8%
G222_M09_1																13.0%	51%	150 bp	0%	15.0
G222_M09_2																12.1%	51%	150 bp	0%	15.0
G222_M09_narrow_MACS2			263	39236
G222_M09_sorted_filtered	21.8	21.8			100%	249 bp	264 bp	0.78%	0.0	21.8	100.0%	100.0%	0.2%	21.8
G222_M10															91.6%
G222_M10_1																14.5%	50%	150 bp	0%	10.2
G222_M10_2																13.5%	50%	150 bp	0%	10.2
G222_M10_narrow_MACS2			247	31345
G222_M10_sorted_filtered	13.5	13.5			100%	233 bp	247 bp	0.79%	0.0	13.5	100.0%	100.0%	0.2%	13.5
G222_M11															94.3%
G222_M11_1																15.2%	51%	150 bp	0%	13.9
G222_M11_2																14.2%	51%	150 bp	0%	13.9
G222_M11_narrow_MACS2			251	39659
G222_M11_sorted_filtered	19.7	19.7			100%	239 bp	252 bp	0.80%	0.0	19.7	100.0%	100.0%	0.2%	19.7
G222_M12															90.2%
G222_M12_1																16.1%	48%	150 bp	9%	16.3
G222_M12_2																15.4%	48%	150 bp	9%	16.3
G222_M12_narrow_MACS2			242	31175
G222_M12_sorted_filtered	20.2	20.2			100%	229 bp	243 bp	0.76%	0.0	20.2	100.0%	100.0%	0.2%	20.2
G222_M16															96.5%
G222_M16_1																13.2%	48%	150 bp	0%	19.1
G222_M16_2																11.4%	48%	150 bp	0%	19.1
G222_M16_narrow_MACS2			286	42904
G222_M16_sorted_filtered	28.9	28.9			100%	275 bp	286 bp	0.82%	0.0	28.9	100.0%	100.0%	0.1%	28.9
G222_M17															96.3%
G222_M17_1																15.9%	43%	150 bp	9%	21.8
G222_M17_2																14.1%	44%	150 bp	9%	21.8
G222_M17_narrow_MACS2			293	27069
G222_M17_sorted_filtered	29.5	29.5			100%	283 bp	293 bp	0.82%	0.0	29.5	100.0%	100.0%	0.2%	29.5
G222_M18															96.3%
G222_M18_1																15.4%	44%	150 bp	0%	11.0
G222_M18_2																13.5%	44%	150 bp	0%	11.0
G222_M18_narrow_MACS2			331	21134
G222_M18_sorted_filtered	14.1	14.1			100%	330 bp	331 bp	0.86%	0.0	14.1	100.0%	100.0%	0.1%	14.1
G222_M19															96.7%
G222_M19_1																15.0%	46%	150 bp	0%	20.3
G222_M19_2																13.8%	46%	150 bp	0%	20.3
G222_M19_narrow_MACS2			301	40140
G222_M19_sorted_filtered	29.3	29.3			100%	294 bp	301 bp	0.77%	0.0	29.3	100.0%	100.0%	0.1%	29.3
G222_M20															96.1%
G222_M20_1																17.4%	45%	150 bp	0%	15.5
G222_M20_2																16.1%	45%	150 bp	0%	15.5
G222_M20_narrow_MACS2			301	27242
G222_M20_sorted_filtered	20.2	20.2			100%	294 bp	302 bp	0.81%	0.0	20.2	100.0%	100.0%	0.2%	20.2
G223_M01D															87.5%
G223_M01D_1																18.1%	48%	150 bp	0%	58.3
G223_M01D_2																16.3%	48%	150 bp	18%	58.3
G223_M01D_narrow_MACS2			272	66217
G223_M01D_sorted_filtered	70.4	70.4			100%	261 bp	273 bp	1.04%	0.0	70.4	100.0%	100.0%	0.5%	70.4
G223_M02															75.1%
G223_M02_1																10.6%	48%	150 bp	9%	13.3
G223_M02_2																10.5%	50%	150 bp	27%	13.3
G223_M02_narrow_MACS2			271	30617
G223_M02_sorted_filtered	13.0	13.0			100%	255 bp	271 bp	2.23%	0.0	13.0	100.0%	100.0%	0.9%	13.0
G223_M03															76.6%
G223_M03_1																12.5%	49%	150 bp	0%	26.2
G223_M03_2																11.6%	50%	150 bp	18%	26.2
G223_M03_narrow_MACS2			259	42511
G223_M03_sorted_filtered	26.7	26.7			100%	244 bp	259 bp	2.66%	0.0	26.7	100.0%	100.0%	1.0%	26.7
G223_M04															71.5%
G223_M04_1																20.3%	50%	150 bp	18%	57.7
G223_M04_2																17.6%	51%	150 bp	36%	57.7
G223_M04_narrow_MACS2			259	58958
G223_M04_sorted_filtered	47.6	47.6			100%	245 bp	259 bp	2.04%	0.0	47.6	100.0%	100.0%	0.9%	47.6
G223_M05															78.7%
G223_M05_1																12.8%	48%	150 bp	9%	9.6
G223_M05_2																12.8%	50%	150 bp	18%	9.6
G223_M05_narrow_MACS2			268	26235
G223_M05_sorted_filtered	9.8	9.8			100%	254 bp	268 bp	2.02%	0.0	9.8	100.0%	100.0%	0.8%	9.8
G223_M06															61.0%
G223_M06_1																27.7%	54%	150 bp	36%	29.1
G223_M06_2																26.6%	58%	150 bp	36%	29.1
G223_M06_narrow_MACS2			260	39020
G223_M06_sorted_filtered	21.9	21.9			100%	242 bp	260 bp	2.55%	0.0	21.9	100.0%	100.0%	1.0%	21.9
G223_M07															80.2%
G223_M07_1																12.2%	52%	150 bp	0%	11.1
G223_M07_2																11.7%	53%	150 bp	9%	11.1
G223_M07_narrow_MACS2			242	28985
G223_M07_sorted_filtered	12.4	12.4			100%	230 bp	242 bp	2.36%	0.0	12.4	100.0%	100.0%	1.0%	12.4
G223_M08															83.8%
G223_M08_1																17.4%	53%	150 bp	9%	31.3
G223_M08_2																16.8%	54%	150 bp	9%	31.3
G223_M08_narrow_MACS2			270	55968
G223_M08_sorted_filtered	37.7	37.7			100%	257 bp	270 bp	1.50%	0.0	37.7	100.0%	100.0%	0.6%	37.7
G223_M09															83.9%
G223_M09_1																18.4%	53%	150 bp	18%	28.2
G223_M09_2																17.3%	53%	150 bp	27%	28.2
G223_M09_narrow_MACS2			272	52267
G223_M09_sorted_filtered	33.2	33.2			100%	259 bp	273 bp	1.05%	0.0	33.2	100.0%	100.0%	0.4%	33.2
G223_M10															85.9%
G223_M10_1																16.5%	48%	150 bp	0%	32.3
G223_M10_2																15.2%	48%	150 bp	9%	32.3
G223_M10_narrow_MACS2			267	51720
G223_M10_sorted_filtered	36.2	36.2			100%	255 bp	267 bp	1.27%	0.0	36.2	100.0%	100.0%	0.6%	36.2
G223_M11															62.1%
G223_M11_1																31.6%	52%	150 bp	36%	39.6
G223_M11_2																29.8%	55%	150 bp	45%	39.6
G223_M11_narrow_MACS2			255	42707
G223_M11_sorted_filtered	28.2	28.2			100%	238 bp	256 bp	1.35%	0.0	28.2	100.0%	100.0%	0.8%	28.2
G223_M12															80.3%
G223_M12_1																20.6%	47%	150 bp	18%	41.6
G223_M12_2																18.6%	48%	150 bp	36%	41.6
G223_M12_narrow_MACS2			266	49249
G223_M12_sorted_filtered	40.7	40.7			100%	252 bp	267 bp	1.33%	0.0	40.7	100.0%	100.0%	0.7%	40.7
G223_M13															76.2%
G223_M13_1																19.8%	48%	150 bp	18%	19.8
G223_M13_2																18.3%	49%	150 bp	27%	19.8
G223_M13_narrow_MACS2			240	36818
G223_M13_sorted_filtered	18.2	18.2			100%	225 bp	240 bp	1.58%	0.0	18.2	100.0%	100.0%	0.8%	18.2
G223_M14															77.0%
G223_M14_1																16.6%	49%	150 bp	9%	16.5
G223_M14_2																15.3%	50%	150 bp	27%	16.5
G223_M14_narrow_MACS2			243	31824
G223_M14_sorted_filtered	15.9	15.9			100%	228 bp	243 bp	2.27%	0.0	15.9	100.0%	100.0%	1.1%	15.9
G223_M15															54.9%
G223_M15_1																30.9%	56%	150 bp	36%	23.6
G223_M15_2																28.9%	60%	150 bp	36%	23.6
G223_M15_narrow_MACS2			247	34640
G223_M15_sorted_filtered	16.4	16.4			100%	230 bp	247 bp	2.33%	0.0	16.4	100.0%	100.0%	1.1%	16.4
G223_M16															71.2%
G223_M16_1																15.6%	49%	150 bp	18%	10.3
G223_M16_2																15.7%	51%	150 bp	27%	10.3
G223_M16_narrow_MACS2			258	23493
G223_M16_sorted_filtered	8.9	8.9			100%	242 bp	258 bp	2.46%	0.0	8.9	100.0%	100.0%	1.0%	8.9
G223_M17															75.0%
G223_M17_1																11.0%	46%	150 bp	0%	9.8
G223_M17_2																10.9%	48%	150 bp	18%	9.8
G223_M17_narrow_MACS2			256	24489
G223_M17_sorted_filtered	9.0	9.0			100%	242 bp	257 bp	2.82%	0.0	9.0	100.0%	100.0%	1.0%	9.0
G223_M18															45.0%
G223_M18_1																56.2%	58%	150 bp	36%	13.6
G223_M18_2																55.7%	66%	150 bp	45%	13.6
G223_M18_narrow_MACS2			236	39550
G223_M18_sorted_filtered	8.2	8.2			100%	224 bp	237 bp	3.26%	0.0	8.2	100.0%	100.0%	1.2%	8.2
G223_M19															77.0%
G223_M19_1																11.1%	48%	150 bp	0%	9.3
G223_M19_2																10.9%	49%	150 bp	18%	9.3
G223_M19_narrow_MACS2			276	23589
G223_M19_sorted_filtered	9.2	9.2			100%	264 bp	277 bp	2.11%	0.0	9.2	100.0%	100.0%	0.8%	9.2
G223_M20															76.4%
G223_M20_1																16.9%	52%	150 bp	9%	23.6
G223_M20_2																15.7%	53%	150 bp	18%	23.6
G223_M20_narrow_MACS2			250	40855
G223_M20_sorted_filtered	24.3	24.3			100%	233 bp	251 bp	1.98%	0.0	24.3	100.0%	100.0%	0.9%	24.3
G223_M21															90.7%
G223_M21_1																14.6%	48%	150 bp	0%	16.5
G223_M21_2																14.4%	48%	150 bp	27%	16.5
G223_M21_narrow_MACS2			303	36571
G223_M21_sorted_filtered	20.8	20.8			100%	295 bp	304 bp	1.05%	0.0	20.8	100.0%	100.0%	0.3%	20.8
G223_M22															82.4%
G223_M22_1																14.1%	48%	150 bp	0%	24.0
G223_M22_2																13.7%	49%	150 bp	18%	24.0
G223_M22_narrow_MACS2			291	38970
G223_M22_sorted_filtered	26.0	26.0			100%	281 bp	291 bp	1.90%	0.0	26.0	100.0%	100.0%	0.7%	26.0
G223_M23															81.9%
G223_M23_1																9.7%	49%	150 bp	0%	12.7
G223_M23_2																9.7%	50%	150 bp	9%	12.7
G223_M23_narrow_MACS2			259	36682
G223_M23_sorted_filtered	15.2	15.2			100%	247 bp	259 bp	2.36%	0.0	15.2	100.0%	100.0%	0.8%	15.2
G223_M24															70.9%
G223_M24_1																14.4%	48%	150 bp	9%	40.1
G223_M24_2																13.3%	50%	150 bp	27%	40.1
G223_M24_narrow_MACS2			266	50133
G223_M24_sorted_filtered	36.5	36.5			100%	248 bp	266 bp	2.56%	0.0	36.5	100.0%	100.0%	1.0%	36.5
G223_M25D															84.2%
G223_M25D_1																19.5%	52%	150 bp	0%	35.2
G223_M25D_2																17.6%	52%	150 bp	18%	35.2
G223_M25D_narrow_MACS2			261	44196
G223_M25D_sorted_filtered	39.9	39.9			100%	244 bp	261 bp	1.33%	0.0	39.9	100.0%	100.0%	0.5%	39.9
G223_M26															89.0%
G223_M26_1																16.4%	53%	150 bp	0%	15.7
G223_M26_2																16.2%	53%	150 bp	18%	15.7
G223_M26_narrow_MACS2			280	35136
G223_M26_sorted_filtered	19.6	19.6			100%	268 bp	280 bp	1.23%	0.0	19.6	100.0%	100.0%	0.4%	19.6
G223_M27															82.9%
G223_M27_1																15.1%	47%	150 bp	0%	45.9
G223_M27_2																14.8%	49%	150 bp	18%	45.9
G223_M27_narrow_MACS2			269	53853
G223_M27_sorted_filtered	50.9	50.9			100%	252 bp	270 bp	2.95%	0.0	50.9	100.0%	100.0%	0.8%	50.9
G223_M28															78.4%
G223_M28_1																9.2%	48%	150 bp	9%	3.0
G223_M28_2																9.7%	49%	150 bp	18%	3.0
G223_M28_narrow_MACS2			275	14709
G223_M28_sorted_filtered	3.1	3.1			100%	261 bp	276 bp	2.94%	0.0	3.1	100.0%	100.0%	0.9%	3.1
G223_M29															83.3%
G223_M29_1																14.8%	48%	150 bp	0%	18.7
G223_M29_2																14.4%	49%	150 bp	18%	18.7
G223_M29_narrow_MACS2			290	35821
G223_M29_sorted_filtered	19.6	19.6			100%	277 bp	290 bp	1.82%	0.0	19.6	100.0%	100.0%	0.5%	19.6
G223_M30D															86.0%
G223_M30D_1																15.5%	47%	150 bp	0%	38.8
G223_M30D_2																14.3%	48%	150 bp	18%	38.8
G223_M30D_narrow_MACS2			264	47169
G223_M30D_sorted_filtered	42.6	42.6			100%	250 bp	265 bp	1.44%	0.0	42.6	100.0%	100.0%	0.6%	42.6
G223_M31															67.2%
G223_M31_1																15.0%	49%	150 bp	18%	13.8
G223_M31_2																13.3%	50%	150 bp	27%	13.8
G223_M31_narrow_MACS2			236	28388
G223_M31_sorted_filtered	11.9	11.9			100%	220 bp	236 bp	3.31%	0.0	11.9	100.0%	100.0%	1.2%	11.9
G223_M32															77.7%
G223_M32_1																10.7%	47%	150 bp	0%	9.4
G223_M32_2																10.1%	48%	150 bp	9%	9.4
G223_M32_narrow_MACS2			257	27349
G223_M32_sorted_filtered	9.5	9.5			100%	240 bp	258 bp	2.79%	0.0	9.5	100.0%	100.0%	1.0%	9.5
G223_M33															73.3%
G223_M33_1																10.3%	47%	150 bp	9%	7.5
G223_M33_2																9.3%	48%	150 bp	18%	7.5
G223_M33_narrow_MACS2			240	25274
G223_M33_sorted_filtered	7.6	7.6			100%	225 bp	240 bp	3.48%	0.0	7.6	100.0%	100.0%	1.1%	7.6
G223_M34															76.0%
G223_M34_1																16.3%	51%	150 bp	27%	14.1
G223_M34_2																14.9%	52%	150 bp	36%	14.1
G223_M34_narrow_MACS2			244	27157
G223_M34_sorted_filtered	14.2	14.2			100%	230 bp	244 bp	1.86%	0.0	14.2	100.0%	100.0%	0.8%	14.2
G223_M35															71.5%
G223_M35_1																10.6%	49%	150 bp	18%	4.5
G223_M35_2																9.5%	50%	150 bp	27%	4.5
G223_M35_narrow_MACS2			255	14371
G223_M35_sorted_filtered	4.1	4.1			100%	241 bp	255 bp	2.88%	0.0	4.1	100.0%	100.0%	1.1%	4.1
G223_M36															75.8%
G223_M36_1																15.4%	48%	150 bp	9%	22.7
G223_M36_2																13.5%	49%	150 bp	18%	22.7
G223_M36_narrow_MACS2			243	41020
G223_M36_sorted_filtered	21.9	21.9			100%	227 bp	243 bp	1.52%	0.0	21.9	100.0%	100.0%	0.8%	21.9
G223_M37															69.2%
G223_M37_1																11.7%	48%	150 bp	18%	12.4
G223_M37_2																10.8%	49%	150 bp	27%	12.4
G223_M37_narrow_MACS2			241	28916
G223_M37_sorted_filtered	10.8	10.8			100%	223 bp	242 bp	2.64%	0.0	10.8	100.0%	100.0%	1.2%	10.8
G223_M38															76.5%
G223_M38_1																16.2%	47%	150 bp	9%	28.9
G223_M38_2																14.1%	47%	150 bp	27%	28.9
G223_M38_narrow_MACS2			257	41889
G223_M38_sorted_filtered	26.8	26.8			100%	244 bp	257 bp	2.02%	0.0	26.8	100.0%	100.0%	0.8%	26.8
G223_M39															77.3%
G223_M39_1																10.1%	47%	150 bp	9%	4.4
G223_M39_2																10.0%	48%	150 bp	18%	4.4
G223_M39_narrow_MACS2			253	15653
G223_M39_sorted_filtered	4.7	4.7			100%	240 bp	253 bp	3.21%	0.0	4.7	100.0%	100.0%	1.0%	4.7
G223_M40															80.0%
G223_M40_1																11.2%	49%	150 bp	9%	5.7
G223_M40_2																11.7%	50%	150 bp	18%	5.7
G223_M40_narrow_MACS2			258	20814
G223_M40_sorted_filtered	6.1	6.1			100%	245 bp	258 bp	2.65%	0.0	6.1	100.0%	100.0%	0.9%	6.1
G223_M41															75.9%
G223_M41_1																9.6%	47%	150 bp	9%	10.9
G223_M41_2																8.7%	47%	150 bp	18%	10.9
G223_M41_narrow_MACS2			235	32075
G223_M41_sorted_filtered	11.7	11.7			100%	222 bp	235 bp	3.72%	0.0	11.7	100.0%	100.0%	1.1%	11.7
G223_M42															87.5%
G223_M42_1																16.4%	52%	150 bp	0%	27.0
G223_M42_2																15.4%	52%	150 bp	9%	27.0
G223_M42_narrow_MACS2			256	54412
G223_M42_sorted_filtered	34.5	34.5			100%	243 bp	257 bp	0.89%	0.0	34.5	100.0%	100.0%	0.4%	34.5
G223_M43D															86.7%
G223_M43D_1																18.6%	51%	150 bp	0%	39.2
G223_M43D_2																17.4%	52%	150 bp	9%	39.2
G223_M43D_narrow_MACS2			264	58291
G223_M43D_sorted_filtered	46.6	46.6			100%	251 bp	264 bp	1.02%	0.0	46.6	100.0%	100.0%	0.4%	46.6
G223_M44															80.1%
G223_M44_1																11.0%	52%	150 bp	9%	6.0
G223_M44_2																11.4%	53%	150 bp	18%	6.0
G223_M44_narrow_MACS2			256	20935
G223_M44_sorted_filtered	6.5	6.5			100%	242 bp	257 bp	2.12%	0.0	6.5	100.0%	100.0%	0.9%	6.5
G223_M45															83.1%
G223_M45_1																25.6%	50%	150 bp	9%	28.0
G223_M45_2																23.7%	51%	150 bp	18%	28.0
G223_M45_narrow_MACS2			243	43190
G223_M45_sorted_filtered	30.0	30.0			100%	231 bp	244 bp	1.17%	0.0	30.0	100.0%	100.0%	0.6%	30.0
G223_M46															65.1%
G223_M46_1																29.2%	52%	150 bp	18%	13.3
G223_M46_2																27.7%	53%	150 bp	36%	13.3
G223_M46_narrow_MACS2			244	31723
G223_M46_sorted_filtered	11.2	11.2			100%	228 bp	244 bp	1.59%	0.0	11.2	100.0%	100.0%	0.8%	11.2
G223_M47															79.1%
G223_M47_1																12.7%	49%	150 bp	0%	5.9
G223_M47_2																12.5%	49%	150 bp	9%	5.9
G223_M47_narrow_MACS2			249	21380
G223_M47_sorted_filtered	5.8	5.8			100%	238 bp	250 bp	1.98%	0.0	5.8	100.0%	100.0%	0.9%	5.8
G223_M48															79.8%
G223_M48_1																14.6%	53%	150 bp	18%	7.1
G223_M48_2																14.5%	53%	150 bp	18%	7.1
G223_M48_narrow_MACS2			241	24076
G223_M48_sorted_filtered	7.5	7.5			100%	230 bp	241 bp	1.87%	0.0	7.5	100.0%	100.0%	0.8%	7.5
G223_M49															62.6%
G223_M49_1																30.8%	49%	150 bp	9%	16.2
G223_M49_2																28.7%	50%	150 bp	27%	16.2
G223_M49_narrow_MACS2			217	37014
G223_M49_sorted_filtered	11.0	11.0			100%	203 bp	218 bp	1.74%	0.0	11.0	100.0%	100.0%	1.2%	11.0

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
\|\|	MACS2	Fragment Length	Fragment Length	`d`	None
\|\|	MACS2	Number of Peaks	Total number of peaks	`peak_count`	None
\|\|	Picard	% Aligned	Percent of aligned reads	`PCT_PF_READS_ALIGNED`	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
\|\|	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
\|\|	Bowtie 2 / HiSAT2	% Aligned	overall alignment rate	`overall_alignment_rate`	None
\|\|	FastQC	% Dups	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC	% GC	Average % GC Content	`percent_gc`	None
\|\|	FastQC	Read Length	Average Read 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

Picard

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

Alignment Summary

Please note that Picard's read counts are divided by two for paired-end data. Total bases (including unaligned) is not provided.

Mean read length

The mean read length of the set of reads examined.

Base Distribution

Plot shows the distribution of bases by cycle.

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

Insert Size

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

Mean Base Quality by Cycle

Plot shows the mean base quality by cycle.

This metric gives an overall snapshot of sequencing machine performance. For most types of sequencing data, the output is expected to show a slight reduction in overall base quality scores towards the end of each read.

Spikes in quality within reads are not expected and may indicate that technical problems occurred during sequencing.

Base Quality Distribution

Plot shows the count of each base quality score.

Samtools

Samtools is a suite of programs for interacting with high-throughput sequencing data.DOI: 10.1093/bioinformatics/btp352.

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.

Bowtie 2 / HiSAT2

Bowtie 2 and HISAT2 are fast and memory-efficient tools for aligning sequencing reads against a reference genome. Unfortunately both tools have identical log output by default, so it is impossible to distiguish which tool was used. .DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4.

Paired-end alignments

This plot shows the number of reads aligning to the reference in different ways.

Please note that single mate alignment counts are halved to tally with pair counts properly.

There are 6 possible types of alignment:

PE mapped uniquely: Pair has only one occurence in the reference genome.
PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
PE one mate mapped uniquely: One read of a pair has one occurence.
PE multimapped: Pair has multiple occurence.
PE one mate multimapped: One read of a pair has multiple occurence.
PE neither mate aligned: Pair has no occurence.

FastQC

FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

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

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 (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.

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:

v1.12

MultiQC Toolbox

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Picard

Alignment Summary

Mean read length

Base Distribution

Insert Size

Mean Base Quality by Cycle

Base Quality Distribution

Samtools

Percent Mapped

Alignment metrics

Samtools Flagstat

Bowtie 2 / HiSAT2

Paired-end alignments

FastQC

Sequence Counts

Sequence Quality Histograms

Per Sequence Quality Scores

Per Base Sequence Content

Rollover for sample name

Per Sequence GC Content

Per Base N Content

Sequence Length Distribution

Sequence Duplication Levels

Overrepresented sequences

Adapter Content

Status Checks

Toggle navigation v1.12

MultiQC Toolbox

Apply Highlight Samples

Apply Rename Samples

Apply Show / Hide Samples

Export Plots

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Tool Citations

About MultiQC

General Statistics

General Statistics: Columns

Picard

Alignment Summary

Mean read length

Base Distribution

Insert Size

Mean Base Quality by Cycle Help

Base Quality Distribution

Samtools

Percent Mapped Help

Alignment metrics

Samtools Flagstat

Bowtie 2 / HiSAT2

Paired-end alignments Help

FastQC

Sequence Counts Help

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

v1.12

Highlight Samples

Rename Samples

Show / Hide Samples

Mean Base Quality by Cycle

Percent Mapped

Paired-end alignments

Sequence Counts

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