Input data and parameters 

QualiMap command line

qualimap bamqc -bam /scratch/108820/ANALYSIS/P4107/piper_ngi/01_raw_alignments/P4107_1006.AHJHNYCCXX.P4107_1006.7.bam -c -nw 400 -hm 3

Alignment

BAM file: /scratch/108820/ANALYSIS/P4107/piper_ngi/01_raw_alignments/P4107_1006.AHJHNYCCXX.P4107_1006.7.bam
Program: bwa (0.7.12-r1039)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Sun Feb 21 08:45:39 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 38,959,933,062 / 29.51%
Number/percentage of C's 26,994,080,681 / 20.45%
Number/percentage of T's 39,160,902,400 / 29.66%
Number/percentage of G's 26,900,131,873 / 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 50.32

Insert size

Mean 30,868.99
Standard Deviation 1,742,369.19
P25/Median/P75 310 / 360 / 410

Mismatches and indels

General error rate 0.78%
Mismatches 978,655,327
Insertions 17,314,440
Deletions 18,576,336
Homopolymer indels 55.48%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
1 249250621 10829861777 43.45 1,247.98
2 243199373 11161911267 45.9 310.2
3 198022430 8670406833 43.78 26.96
4 191154276 8754918963 45.8 493.43
5 180915260 7909203520 43.72 20.34
6 171115067 7617404526 44.52 255.5
7 159138663 7038411044 44.23 219.93
8 146364022 6913015746 47.23 1,559.74
9 141213431 5448755129 38.59 261.79
10 135534747 6922791668 51.08 986.3
11 135006516 6010071614 44.52 222.78
12 133851895 5956110555 44.5 23.22
13 115169878 4211746627 36.57 18.53
14 107349540 4013198973 37.38 25.28
15 102531392 3765263230 36.72 23.79
16 90354753 4036100939 44.67 256.74
17 81195210 3664247194 45.13 153.61
18 78077248 3419975143 43.8 211.51
19 59128983 2670087274 45.16 586.83
20 63025520 2728398882 43.29 120.42
21 48129895 1770539071 36.79 191.22
22 51304566 1610781614 31.4 137.44
X 155270560 3487015457 22.46 60.97
Y 59373566 1395790549 23.51 557.66
MT 16569 320070887 19,317.45 1,248.86
GL000207.1 4262 291699 68.44 75.51
GL000226.1 15008 247077639 16,463.06 13,113.08
GL000229.1 19913 3657317 183.66 91.43
GL000231.1 27386 5144748 187.86 108.6
GL000210.1 27682 559736 20.22 8.52
GL000239.1 33824 4041164 119.48 64.2
GL000235.1 34474 5891825 170.91 160.64
GL000201.1 36148 725673 20.08 11.41
GL000247.1 36422 2202391 60.47 32.39
GL000245.1 36651 4160939 113.53 59.46
GL000197.1 37175 795985 21.41 5.83
GL000203.1 37498 2390468 63.75 52.04
GL000246.1 38154 1106993 29.01 10.49
GL000249.1 38502 839925 21.82 6.06
GL000196.1 38914 854230 21.95 5.7
GL000248.1 39786 846963 21.29 9.81
GL000244.1 39929 1571442 39.36 19.61
GL000238.1 39939 978313 24.5 10
GL000202.1 40103 1239786 30.92 11.28
GL000234.1 40531 9358538 230.9 88.36
GL000232.1 40652 12650706 311.2 118.18
GL000206.1 41001 1046331 25.52 9.66
GL000240.1 41933 3093881 73.78 38.15
GL000236.1 41934 1504622 35.88 17.57
GL000241.1 42152 10231898 242.74 125.25
GL000243.1 43341 4076366 94.05 69.96
GL000242.1 43523 868080 19.95 8.81
GL000230.1 43691 3675259 84.12 30.07
GL000237.1 45867 6233156 135.9 58.74
GL000233.1 45941 4274409 93.04 35.85
GL000204.1 81310 2880134 35.42 13.82
GL000198.1 90085 14665244 162.79 192.38
GL000208.1 92689 22189999 239.4 673.39
GL000191.1 106433 2885919 27.11 11.75
GL000227.1 128374 2733199 21.29 12.82
GL000228.1 129120 44086320 341.44 2,224.98
GL000214.1 137718 31551673 229.1 190.35
GL000221.1 155397 19213665 123.64 69.95
GL000209.1 159169 3742835 23.51 6.5
GL000218.1 161147 16568942 102.82 35.1
GL000220.1 161802 363594822 2,247.16 3,221.17
GL000213.1 164239 3148770 19.17 8.6
GL000211.1 166566 9286398 55.75 22.79
GL000199.1 169874 376560009 2,216.7 5,438.65
GL000217.1 172149 12162098 70.65 41.56
GL000216.1 172294 99866705 579.63 3,041.97
GL000215.1 172545 3285176 19.04 9.12
GL000205.1 174588 27334911 156.57 83.93
GL000219.1 179198 24140602 134.71 113.49
GL000224.1 179693 43242619 240.65 407.61
GL000223.1 180455 4264922 23.63 7.5
GL000195.1 182896 31497356 172.21 56.83
GL000212.1 186858 80912466 433.02 5,800.21
GL000222.1 186861 12852403 68.78 244.39
GL000200.1 187035 2824280 15.1 7.24
GL000193.1 189789 21762680 114.67 62.17
GL000194.1 191469 22674330 118.42 60.42
GL000225.1 211173 106205873 502.93 1,259.43
GL000192.1 547496 23228524 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