Input data and parameters 

QualiMap command line

qualimap bamqc -bam /scratch/108816/ANALYSIS/P4107/piper_ngi/01_raw_alignments/P4107_1004.AHJHNYCCXX.P4107_1004.5.bam -c -nw 400 -hm 3

Alignment

BAM file: /scratch/108816/ANALYSIS/P4107/piper_ngi/01_raw_alignments/P4107_1004.AHJHNYCCXX.P4107_1004.5.bam
Program: bwa (0.7.12-r1039)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Sun Feb 21 04:37:04 CET 2016
Draw chromosome limits: yes

Summary 

Globals

Reference size 3,101,804,739
Number of reads 1,002,828,927
Mapped reads 985,115,356 / 98.23%
Unmapped reads 17,713,571 / 1.77%
Paired reads 985,115,356 / 98.23%
Mapped reads, only first in pair 492,578,290 / 49.12%
Mapped reads, only second in pair 492,537,066 / 49.11%
Mapped reads, both in pair 984,087,603 / 98.13%
Mapped reads, singletons 1,027,753 / 0.1%
Read min/max/mean length 30 / 151 / 150.37
Clipped reads 57,747,243 / 5.76%
Duplication rate 45.1%

ACGT Content

Number/percentage of A's 43,241,669,606 / 29.65%
Number/percentage of C's 29,624,033,977 / 20.31%
Number/percentage of T's 43,463,116,238 / 29.8%
Number/percentage of G's 29,506,786,562 / 20.23%
Number/percentage of N's 0 / 0%
GC Percentage 40.55%

Coverage

Mean 47.04
Standard Deviation 663.35

Mapping Quality

Mean Mapping Quality 50.36

Insert size

Mean 28,252.39
Standard Deviation 1,644,630.96
P25/Median/P75 312 / 361 / 410

Mismatches and indels

General error rate 0.68%
Mismatches 932,823,577
Insertions 19,653,759
Deletions 20,783,575
Homopolymer indels 56.06%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
1 249250621 11921707944 47.83 1,365.48
2 243199373 12336985885 50.73 303.71
3 198022430 9624314420 48.6 30.27
4 191154276 9779653579 51.16 555.73
5 180915260 8780143103 48.53 23.64
6 171115067 8448298269 49.37 278.17
7 159138663 7774212876 48.85 239.26
8 146364022 7697427041 52.59 1,864.27
9 141213431 6015345737 42.6 286.7
10 135534747 7630121097 56.3 1,097.7
11 135006516 6633173872 49.13 250.7
12 133851895 6581654645 49.17 26.9
13 115169878 4693703152 40.75 21.67
14 107349540 4438803749 41.35 28.58
15 102531392 4137018335 40.35 26.89
16 90354753 4404849707 48.75 290.53
17 81195210 3980017746 49.02 167.35
18 78077248 3788675015 48.52 232.11
19 59128983 2878052334 48.67 645.45
20 63025520 2974488951 47.19 137.68
21 48129895 1957869447 40.68 213.5
22 51304566 1737325750 33.86 148.31
X 155270560 3871712078 24.94 67.76
Y 59373566 1542991071 25.99 625.51
MT 16569 345179039 20,832.82 1,361.24
GL000207.1 4262 304621 71.47 71.7
GL000226.1 15008 269125259 17,932.12 14,405.79
GL000229.1 19913 3984649 200.1 99.07
GL000231.1 27386 5691378 207.82 122.89
GL000210.1 27682 611222 22.08 9.35
GL000239.1 33824 4395437 129.95 75
GL000235.1 34474 6573998 190.69 172.04
GL000201.1 36148 758900 20.99 12.93
GL000247.1 36422 2356335 64.7 35.78
GL000245.1 36651 4735185 129.2 67.52
GL000197.1 37175 878145 23.62 6.97
GL000203.1 37498 2800602 74.69 61.35
GL000246.1 38154 1210486 31.73 12.65
GL000249.1 38502 884769 22.98 6.85
GL000196.1 38914 949206 24.39 7.7
GL000248.1 39786 936527 23.54 10.94
GL000244.1 39929 1770559 44.34 22.19
GL000238.1 39939 1118994 28.02 11.03
GL000202.1 40103 1349542 33.65 15.1
GL000234.1 40531 10360595 255.62 100.79
GL000232.1 40652 13952740 343.22 130.71
GL000206.1 41001 1086159 26.49 11.14
GL000240.1 41933 3391686 80.88 42.82
GL000236.1 41934 1680184 40.07 20.65
GL000241.1 42152 11489208 272.57 147
GL000243.1 43341 4540607 104.76 76.66
GL000242.1 43523 884369 20.32 9.24
GL000230.1 43691 4037984 92.42 34.4
GL000237.1 45867 6732715 146.79 64.76
GL000233.1 45941 4613475 100.42 40.31
GL000204.1 81310 2966628 36.49 14.98
GL000198.1 90085 16115894 178.9 212.92
GL000208.1 92689 24663367 266.09 744.33
GL000191.1 106433 3085569 28.99 13.52
GL000227.1 128374 3104309 24.18 14.51
GL000228.1 129120 45958633 355.94 2,293.81
GL000214.1 137718 34409795 249.86 197.34
GL000221.1 155397 21617724 139.11 80.53
GL000209.1 159169 4019715 25.25 8.68
GL000218.1 161147 18308063 113.61 39.79
GL000220.1 161802 402660422 2,488.6 3,494.9
GL000213.1 164239 3526499 21.47 10.24
GL000211.1 166566 10422773 62.57 26.1
GL000199.1 169874 418940847 2,466.19 6,087.72
GL000217.1 172149 13611436 79.07 47.21
GL000216.1 172294 106979577 620.91 3,282.9
GL000215.1 172545 3599762 20.86 10.36
GL000205.1 174588 29845651 170.95 92.82
GL000219.1 179198 26802218 149.57 126.38
GL000224.1 179693 46231937 257.28 432.94
GL000223.1 180455 4602433 25.5 8.6
GL000195.1 182896 34669839 189.56 63.84
GL000212.1 186858 89378113 478.32 6,438.03
GL000222.1 186861 13888253 74.32 258.5
GL000200.1 187035 3113269 16.65 8.45
GL000193.1 189789 23842938 125.63 67.27
GL000194.1 191469 24934556 130.23 67.03
GL000225.1 211173 110774724 524.57 1,300.36
GL000192.1 547496 25510296 46.59 24.5

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