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 |