Input data and parameters 

QualiMap command line

qualimap bamqc -bam /scratch/108825/ANALYSIS/P4107/piper_ngi/01_raw_alignments/P4107_1002.AHJHNYCCXX.P4107_1002.3.bam -c -nw 400 -hm 3

Alignment

BAM file: /scratch/108825/ANALYSIS/P4107/piper_ngi/01_raw_alignments/P4107_1002.AHJHNYCCXX.P4107_1002.3.bam
Program: bwa (0.7.12-r1039)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Sun Feb 21 10:11:04 CET 2016
Draw chromosome limits: yes

Summary 

Globals

Reference size 3,101,804,739
Number of reads 865,975,844
Mapped reads 847,067,526 / 97.82%
Unmapped reads 18,908,318 / 2.18%
Paired reads 847,067,526 / 97.82%
Mapped reads, only first in pair 423,736,526 / 48.93%
Mapped reads, only second in pair 423,331,000 / 48.88%
Mapped reads, both in pair 845,777,619 / 97.67%
Mapped reads, singletons 1,289,907 / 0.15%
Read min/max/mean length 30 / 151 / 150.37
Clipped reads 54,256,947 / 6.27%
Duplication rate 20.69%

ACGT Content

Number/percentage of A's 36,927,152,059 / 29.5%
Number/percentage of C's 25,613,258,425 / 20.46%
Number/percentage of T's 37,117,969,095 / 29.65%
Number/percentage of G's 25,511,735,846 / 20.38%
Number/percentage of N's 0 / 0%
GC Percentage 40.84%

Coverage

Mean 40.38
Standard Deviation 546.29

Mapping Quality

Mean Mapping Quality 50.32

Insert size

Mean 29,316.94
Standard Deviation 1,671,881.27
P25/Median/P75 315 / 364 / 415

Mismatches and indels

General error rate 0.8%
Mismatches 945,349,326
Insertions 16,421,563
Deletions 17,388,962
Homopolymer indels 55.52%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
1 249250621 10269453866 41.2 1,174.31
2 243199373 10570497115 43.46 265.51
3 198022430 8221710564 41.52 25.66
4 191154276 8293096267 43.38 461.45
5 180915260 7495338328 41.43 19.13
6 171115067 7217824316 42.18 242.49
7 159138663 6672796021 41.93 207.9
8 146364022 6542102600 44.7 1,435.87
9 141213431 5172041791 36.63 246.08
10 135534747 6560065683 48.4 919.93
11 135006516 5697080378 42.2 209.63
12 133851895 5648283911 42.2 22
13 115169878 3991850242 34.66 17.58
14 107349540 3807018240 35.46 23.71
15 102531392 3573620425 34.85 22.52
16 90354753 3832943580 42.42 240.89
17 81195210 3482952366 42.9 145.45
18 78077248 3242685283 41.53 200.35
19 59128983 2544232485 43.03 556.93
20 63025520 2589166857 41.08 115.83
21 48129895 1677746648 34.86 182.97
22 51304566 1531899186 29.86 130.8
X 155270560 3303833952 21.28 57.12
Y 59373566 1322567755 22.28 524.63
MT 16569 304187388 18,358.83 1,180.84
GL000207.1 4262 283979 66.63 71.19
GL000226.1 15008 232926234 15,520.14 12,334.76
GL000229.1 19913 3482441 174.88 81.7
GL000231.1 27386 4870738 177.86 102.74
GL000210.1 27682 541182 19.55 7.9
GL000239.1 33824 3768623 111.42 61.28
GL000235.1 34474 5633320 163.41 151.72
GL000201.1 36148 671331 18.57 9.22
GL000247.1 36422 2113650 58.03 30.48
GL000245.1 36651 4041805 110.28 58.24
GL000197.1 37175 757229 20.37 5.42
GL000203.1 37498 2267158 60.46 50.05
GL000246.1 38154 1088122 28.52 10.32
GL000249.1 38502 771459 20.04 5.34
GL000196.1 38914 792320 20.36 5.59
GL000248.1 39786 831164 20.89 9.07
GL000244.1 39929 1504248 37.67 19.05
GL000238.1 39939 950214 23.79 9.17
GL000202.1 40103 1205185 30.05 12.49
GL000234.1 40531 8949369 220.8 83.26
GL000232.1 40652 12080831 297.18 112.99
GL000206.1 41001 1005580 24.53 9.08
GL000240.1 41933 2920957 69.66 35.21
GL000236.1 41934 1423050 33.94 16.83
GL000241.1 42152 9607783 227.93 119.29
GL000243.1 43341 3893966 89.84 67.6
GL000242.1 43523 818234 18.8 8.23
GL000230.1 43691 3442427 78.79 27.37
GL000237.1 45867 5948579 129.69 57.84
GL000233.1 45941 4043068 88.01 33.72
GL000204.1 81310 2652014 32.62 13.79
GL000198.1 90085 13645006 151.47 179.87
GL000208.1 92689 20963037 226.17 629.63
GL000191.1 106433 2787780 26.19 11.55
GL000227.1 128374 2576918 20.07 11.99
GL000228.1 129120 42743518 331.04 2,166.28
GL000214.1 137718 29964222 217.58 179.41
GL000221.1 155397 18101964 116.49 65.63
GL000209.1 159169 3499519 21.99 5.95
GL000218.1 161147 15644042 97.08 33.65
GL000220.1 161802 348438866 2,153.49 3,074.79
GL000213.1 164239 2901227 17.66 7.96
GL000211.1 166566 8929782 53.61 21.03
GL000199.1 169874 355809388 2,094.55 5,096.6
GL000217.1 172149 11376910 66.09 39.28
GL000216.1 172294 95537428 554.5 2,909.24
GL000215.1 172545 3100163 17.97 8.6
GL000205.1 174588 25704431 147.23 80.45
GL000219.1 179198 22887540 127.72 107.49
GL000224.1 179693 40875824 227.48 387.75
GL000223.1 180455 4026304 22.31 7.17
GL000195.1 182896 30188770 165.06 55
GL000212.1 186858 76900249 411.54 5,488.89
GL000222.1 186861 12270475 65.67 240.25
GL000200.1 187035 2672002 14.29 7.05
GL000193.1 189789 20614303 108.62 59.3
GL000194.1 191469 21173205 110.58 55.41
GL000225.1 211173 102288477 484.38 1,212.49
GL000192.1 547496 22016531 40.21 20.58

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