Input data and parameters 

QualiMap command line

qualimap bamqc -bam /scratch/108820/ANALYSIS/P4107/piper_ngi/05_processed_alignments/P4107_1006.clean.dedup.bam -c -nw 400 -hm 3

Alignment

BAM file: /scratch/108820/ANALYSIS/P4107/piper_ngi/05_processed_alignments/P4107_1006.clean.dedup.bam
Program: bwa (0.7.12-r1039)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Wed Feb 24 21:00:00 CET 2016
Draw chromosome limits: yes

Summary 

Globals

Reference size 3,101,804,739
Number of reads 912,383,669
Mapped reads 894,970,438 / 98.09%
Unmapped reads 17,413,231 / 1.91%
Paired reads 894,970,438 / 98.09%
Mapped reads, only first in pair 447,733,402 / 49.07%
Mapped reads, only second in pair 447,237,036 / 49.02%
Mapped reads, both in pair 893,549,932 / 97.94%
Mapped reads, singletons 1,420,506 / 0.16%
Read min/max/mean length 30 / 151 / 150.37
Clipped reads 64,443,293 / 7.06%
Duplication rate 23.24%

ACGT Content

Number/percentage of A's 38,959,134,016 / 29.51%
Number/percentage of C's 26,993,680,504 / 20.45%
Number/percentage of T's 39,160,075,074 / 29.66%
Number/percentage of G's 26,899,717,550 / 20.38%
Number/percentage of N's 0 / 0%
GC Percentage 40.82%

Coverage

Mean 42.59
Standard Deviation 586.38

Mapping Quality

Mean Mapping Quality 50.33

Insert size

Mean 30,869.34
Standard Deviation 1,742,379.2
P25/Median/P75 310 / 360 / 410

Mismatches and indels

General error rate 0.78%
Mismatches 975,601,150
Insertions 17,714,581
Deletions 18,840,321
Homopolymer indels 55.39%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
1 249250621 10829835549 43.45 1,247.98
2 243199373 11161883342 45.9 310.2
3 198022430 8670382898 43.78 26.96
4 191154276 8754923152 45.8 493.43
5 180915260 7909198671 43.72 20.33
6 171115067 7617397833 44.52 255.49
7 159138663 7038404925 44.23 219.93
8 146364022 6912993420 47.23 1,559.74
9 141213431 5448743936 38.59 261.79
10 135534747 6922783556 51.08 986.3
11 135006516 6010064473 44.52 222.78
12 133851895 5956087799 44.5 23.22
13 115169878 4211730206 36.57 18.52
14 107349540 4013206336 37.38 25.27
15 102531392 3765256168 36.72 23.79
16 90354753 4036095971 44.67 256.74
17 81195210 3664222313 45.13 153.61
18 78077248 3419973990 43.8 211.51
19 59128983 2670076347 45.16 586.83
20 63025520 2728397026 43.29 120.42
21 48129895 1770536627 36.79 191.22
22 51304566 1610779905 31.4 137.44
X 155270560 3487018977 22.46 60.97
Y 59373566 1395790021 23.51 557.66
MT 16569 320070887 19,317.45 1,248.86
GL000207.1 4262 291699 68.44 75.51
GL000226.1 15008 247077641 16,463.06 13,113.08
GL000229.1 19913 3657176 183.66 91.42
GL000231.1 27386 5144728 187.86 108.6
GL000210.1 27682 559736 20.22 8.52
GL000239.1 33824 4041163 119.48 64.2
GL000235.1 34474 5891829 170.91 160.64
GL000201.1 36148 725673 20.08 11.41
GL000247.1 36422 2202668 60.48 32.37
GL000245.1 36651 4160944 113.53 59.46
GL000197.1 37175 795985 21.41 5.83
GL000203.1 37498 2390738 63.76 52.04
GL000246.1 38154 1107005 29.01 10.49
GL000249.1 38502 839925 21.82 6.06
GL000196.1 38914 854230 21.95 5.7
GL000248.1 39786 846965 21.29 9.81
GL000244.1 39929 1571445 39.36 19.61
GL000238.1 39939 978303 24.49 10
GL000202.1 40103 1240036 30.92 11.26
GL000234.1 40531 9358985 230.91 88.35
GL000232.1 40652 12651003 311.2 118.13
GL000206.1 41001 1046331 25.52 9.66
GL000240.1 41933 3093894 73.78 38.15
GL000236.1 41934 1504623 35.88 17.57
GL000241.1 42152 10231865 242.74 125.25
GL000243.1 43341 4076366 94.05 69.96
GL000242.1 43523 868084 19.95 8.81
GL000230.1 43691 3675379 84.12 30.06
GL000237.1 45867 6233371 135.9 58.7
GL000233.1 45941 4274411 93.04 35.85
GL000204.1 81310 2880132 35.42 13.82
GL000198.1 90085 14665260 162.79 192.38
GL000208.1 92689 22190039 239.4 673.39
GL000191.1 106433 2885910 27.11 11.75
GL000227.1 128374 2733197 21.29 12.82
GL000228.1 129120 44086331 341.44 2,224.98
GL000214.1 137718 31551743 229.1 190.35
GL000221.1 155397 19213720 123.64 69.95
GL000209.1 159169 3742819 23.51 6.5
GL000218.1 161147 16569047 102.82 35.1
GL000220.1 161802 363596212 2,247.17 3,221.15
GL000213.1 164239 3148975 19.17 8.6
GL000211.1 166566 9286160 55.75 22.79
GL000199.1 169874 376560032 2,216.7 5,438.65
GL000217.1 172149 12162312 70.65 41.56
GL000216.1 172294 99865872 579.62 3,041.97
GL000215.1 172545 3285175 19.04 9.12
GL000205.1 174588 27335397 156.57 83.93
GL000219.1 179198 24141646 134.72 113.49
GL000224.1 179693 43238362 240.62 407.6
GL000223.1 180455 4264924 23.63 7.5
GL000195.1 182896 31498117 172.22 56.82
GL000212.1 186858 80912410 433.02 5,800.21
GL000222.1 186861 12852518 68.78 244.39
GL000200.1 187035 2824280 15.1 7.24
GL000193.1 189789 21762533 114.67 62.17
GL000194.1 191469 22674523 118.42 60.41
GL000225.1 211173 106205977 502.93 1,259.43
GL000192.1 547496 23228432 42.43 21.23

Coverage across reference 

Coverage Histogram 

Coverage Histogram (0-50X) 

Genome Fraction Coverage 

Duplication Rate Histogram 

Mapped Reads Nucleotide Content 

Mapped Reads GC-content Distribution 

Mapped Reads Clipping Profile 

Homopolymer Indels 

Mapping Quality Across Reference 

Mapping Quality Histogram 

Insert Size Across Reference 

Insert Size Histogram