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 |