Input data and parameters 

QualiMap command line

qualimap bamqc -bam /scratch/108823/ANALYSIS/P4107/piper_ngi/01_raw_alignments/P4107_1001.AHJHNYCCXX.P4107_1001.2.bam -c -nw 400 -hm 3

Alignment

BAM file: /scratch/108823/ANALYSIS/P4107/piper_ngi/01_raw_alignments/P4107_1001.AHJHNYCCXX.P4107_1001.2.bam
Program: bwa (0.7.12-r1039)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Sun Feb 21 07:38:35 CET 2016
Draw chromosome limits: yes

Summary 

Globals

Reference size 3,101,804,739
Number of reads 772,071,557
Mapped reads 751,147,332 / 97.29%
Unmapped reads 20,924,225 / 2.71%
Paired reads 751,147,332 / 97.29%
Mapped reads, only first in pair 375,903,971 / 48.69%
Mapped reads, only second in pair 375,243,361 / 48.6%
Mapped reads, both in pair 749,705,894 / 97.1%
Mapped reads, singletons 1,441,438 / 0.19%
Read min/max/mean length 30 / 151 / 150.39
Clipped reads 50,331,843 / 6.52%
Duplication rate 16.61%

ACGT Content

Number/percentage of A's 32,673,650,686 / 29.46%
Number/percentage of C's 22,733,145,070 / 20.5%
Number/percentage of T's 32,842,002,062 / 29.62%
Number/percentage of G's 22,647,678,571 / 20.42%
Number/percentage of N's 0 / 0%
GC Percentage 40.92%

Coverage

Mean 35.78
Standard Deviation 491.12

Mapping Quality

Mean Mapping Quality 50.31

Insert size

Mean 28,931.34
Standard Deviation 1,662,610.5
P25/Median/P75 306 / 355 / 406

Mismatches and indels

General error rate 0.8%
Mismatches 838,810,906
Insertions 14,499,218
Deletions 15,346,788
Homopolymer indels 55.55%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
1 249250621 9105502622 36.53 1,068
2 243199373 9356230846 38.47 243.97
3 198022430 7270460429 36.72 22.36
4 191154276 7330874621 38.35 417.4
5 180915260 6626088972 36.63 17.1
6 171115067 6390558852 37.35 217.38
7 159138663 5915367321 37.17 189.38
8 146364022 5786155376 39.53 1,261.57
9 141213431 4582297851 32.45 225.75
10 135534747 5828759626 43.01 840.04
11 135006516 5045937352 37.38 187.55
12 133851895 5004655819 37.39 19.58
13 115169878 3525269623 30.61 15.7
14 107349540 3372544531 31.42 21.18
15 102531392 3171436974 30.93 20.09
16 90354753 3408253041 37.72 215.83
17 81195210 3100350094 38.18 132.46
18 78077248 2870800933 36.77 181.19
19 59128983 2271968712 38.42 505.03
20 63025520 2300126300 36.5 103.18
21 48129895 1488018477 30.92 162.56
22 51304566 1367150742 26.65 117.18
X 155270560 2919824567 18.8 51.59
Y 59373566 1167393095 19.66 472.08
MT 16569 267319881 16,133.74 1,077.11
GL000207.1 4262 245550 57.61 62.16
GL000226.1 15008 208799844 13,912.57 11,083.66
GL000229.1 19913 3159908 158.69 79.07
GL000231.1 27386 4328012 158.04 90.97
GL000210.1 27682 443325 16.01 7.04
GL000239.1 33824 3335011 98.6 51.47
GL000235.1 34474 4970709 144.19 145.48
GL000201.1 36148 604223 16.72 9.56
GL000247.1 36422 1806811 49.61 26.45
GL000245.1 36651 3592176 98.01 52.95
GL000197.1 37175 706092 18.99 5.22
GL000203.1 37498 1976955 52.72 43.63
GL000246.1 38154 941283 24.67 9.6
GL000249.1 38502 702256 18.24 5.08
GL000196.1 38914 724072 18.61 5.31
GL000248.1 39786 737555 18.54 8.09
GL000244.1 39929 1329642 33.3 17.02
GL000238.1 39939 836883 20.95 8.19
GL000202.1 40103 1027431 25.62 10.95
GL000234.1 40531 7957901 196.34 75.94
GL000232.1 40652 10564169 259.87 98.72
GL000206.1 41001 898020 21.9 8.87
GL000240.1 41933 2601993 62.05 32.89
GL000236.1 41934 1283508 30.61 14.9
GL000241.1 42152 8544986 202.72 107.75
GL000243.1 43341 3449403 79.59 57.86
GL000242.1 43523 715960 16.45 7.41
GL000230.1 43691 3039186 69.56 24.01
GL000237.1 45867 5240326 114.25 50.84
GL000233.1 45941 3575938 77.84 29.99
GL000204.1 81310 2332876 28.69 11.79
GL000198.1 90085 12126520 134.61 160.15
GL000208.1 92689 18765897 202.46 566.6
GL000191.1 106433 2428156 22.81 9.94
GL000227.1 128374 2343660 18.26 10.99
GL000228.1 129120 38935461 301.54 1,968.31
GL000214.1 137718 26470572 192.21 159.85
GL000221.1 155397 16047354 103.27 58.3
GL000209.1 159169 3117207 19.58 5.86
GL000218.1 161147 13934629 86.47 29.67
GL000220.1 161802 311219504 1,923.46 2,724.98
GL000213.1 164239 2571382 15.66 7.2
GL000211.1 166566 7725935 46.38 18.79
GL000199.1 169874 318433202 1,874.53 4,623.22
GL000217.1 172149 10058350 58.43 34.62
GL000216.1 172294 86086855 499.65 2,629.95
GL000215.1 172545 2711170 15.71 7.61
GL000205.1 174588 23086394 132.23 71.55
GL000219.1 179198 20345936 113.54 95.9
GL000224.1 179693 36545552 203.38 344.47
GL000223.1 180455 3575866 19.82 6.49
GL000195.1 182896 26579987 145.33 47.37
GL000212.1 186858 68692615 367.62 4,950.42
GL000222.1 186861 10997549 58.85 217.34
GL000200.1 187035 2371917 12.68 6.49
GL000193.1 189789 18259439 96.21 53.02
GL000194.1 191469 19047039 99.48 50.3
GL000225.1 211173 93650473 443.48 1,123.8
GL000192.1 547496 19491598 35.6 18.17

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