Input data and parameters 

QualiMap command line

qualimap bamqc -bam /scratch/108816/ANALYSIS/P4107/piper_ngi/05_processed_alignments/P4107_1004.clean.dedup.bam -c -nw 400 -hm 3

Alignment

BAM file: /scratch/108816/ANALYSIS/P4107/piper_ngi/05_processed_alignments/P4107_1004.clean.dedup.bam
Program: bwa (0.7.12-r1039)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Wed Feb 24 15:56:42 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 43,240,749,864 / 29.65%
Number/percentage of C's 29,623,578,341 / 20.31%
Number/percentage of T's 43,462,153,420 / 29.8%
Number/percentage of G's 29,506,313,928 / 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 50.37

Insert size

Mean 28,253.13
Standard Deviation 1,644,652.56
P25/Median/P75 312 / 361 / 410

Mismatches and indels

General error rate 0.68%
Mismatches 929,597,624
Insertions 20,113,669
Deletions 21,074,591
Homopolymer indels 55.95%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
1 249250621 11921690737 47.83 1,365.48
2 243199373 12336955887 50.73 303.71
3 198022430 9624278300 48.6 30.27
4 191154276 9779641285 51.16 555.73
5 180915260 8780134000 48.53 23.63
6 171115067 8448270059 49.37 278.17
7 159138663 7774193420 48.85 239.26
8 146364022 7697406891 52.59 1,864.27
9 141213431 6015332640 42.6 286.7
10 135534747 7630104551 56.3 1,097.7
11 135006516 6633160131 49.13 250.7
12 133851895 6581632331 49.17 26.9
13 115169878 4693689684 40.75 21.66
14 107349540 4438798290 41.35 28.58
15 102531392 4137004115 40.35 26.89
16 90354753 4404840940 48.75 290.53
17 81195210 3979999799 49.02 167.35
18 78077248 3788659485 48.52 232.11
19 59128983 2878037673 48.67 645.45
20 63025520 2974469434 47.19 137.68
21 48129895 1957869761 40.68 213.5
22 51304566 1737328742 33.86 148.31
X 155270560 3871716588 24.94 67.76
Y 59373566 1542992068 25.99 625.51
MT 16569 345179039 20,832.82 1,361.24
GL000207.1 4262 304619 71.47 71.69
GL000226.1 15008 269125263 17,932.12 14,405.78
GL000229.1 19913 3984466 200.09 99.07
GL000231.1 27386 5691361 207.82 122.89
GL000210.1 27682 611222 22.08 9.35
GL000239.1 33824 4395433 129.95 75
GL000235.1 34474 6574031 190.7 172.04
GL000201.1 36148 758900 20.99 12.93
GL000247.1 36422 2356314 64.69 35.78
GL000245.1 36651 4735188 129.2 67.52
GL000197.1 37175 878145 23.62 6.97
GL000203.1 37498 2800867 74.69 61.36
GL000246.1 38154 1210492 31.73 12.65
GL000249.1 38502 884769 22.98 6.85
GL000196.1 38914 949206 24.39 7.7
GL000248.1 39786 936525 23.54 10.94
GL000244.1 39929 1770557 44.34 22.19
GL000238.1 39939 1118986 28.02 11.03
GL000202.1 40103 1349534 33.65 15.1
GL000234.1 40531 10360582 255.62 100.79
GL000232.1 40652 13952096 343.21 130.72
GL000206.1 41001 1086159 26.49 11.14
GL000240.1 41933 3391681 80.88 42.82
GL000236.1 41934 1680180 40.07 20.65
GL000241.1 42152 11489092 272.56 147
GL000243.1 43341 4540652 104.77 76.66
GL000242.1 43523 884381 20.32 9.24
GL000230.1 43691 4038718 92.44 34.37
GL000237.1 45867 6732844 146.79 64.74
GL000233.1 45941 4613495 100.42 40.31
GL000204.1 81310 2966690 36.49 14.98
GL000198.1 90085 16116011 178.9 212.92
GL000208.1 92689 24663364 266.09 744.33
GL000191.1 106433 3085527 28.99 13.52
GL000227.1 128374 3104256 24.18 14.51
GL000228.1 129120 45958682 355.94 2,293.81
GL000214.1 137718 34409870 249.86 197.34
GL000221.1 155397 21617609 139.11 80.53
GL000209.1 159169 4019694 25.25 8.68
GL000218.1 161147 18308083 113.61 39.79
GL000220.1 161802 402660819 2,488.6 3,494.89
GL000213.1 164239 3526683 21.47 10.24
GL000211.1 166566 10422912 62.58 26.09
GL000199.1 169874 418940809 2,466.19 6,087.72
GL000217.1 172149 13611627 79.07 47.21
GL000216.1 172294 106978769 620.91 3,282.9
GL000215.1 172545 3599755 20.86 10.36
GL000205.1 174588 29847023 170.96 92.8
GL000219.1 179198 26802269 149.57 126.38
GL000224.1 179693 46232539 257.29 432.93
GL000223.1 180455 4602437 25.5 8.6
GL000195.1 182896 34670052 189.56 63.83
GL000212.1 186858 89378027 478.32 6,438.03
GL000222.1 186861 13888218 74.32 258.5
GL000200.1 187035 3113269 16.65 8.45
GL000193.1 189789 23842907 125.63 67.27
GL000194.1 191469 24934839 130.23 67.02
GL000225.1 211173 110774792 524.57 1,300.36
GL000192.1 547496 25510280 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