Input data and parameters
QualiMap command line
qualimap bamqc -bam /scratch/108820/ANALYSIS/P4107/piper_ngi/05_processed_alignments/P4107_1006.clean.dedup.bam -c -nw 400 -hm 3 |
Alignment
BAM file: | /scratch/108820/ANALYSIS/P4107/piper_ngi/05_processed_alignments/P4107_1006.clean.dedup.bam |
Program: | bwa (0.7.12-r1039) |
Size of a homopolymer: | 3 |
Number of windows: | 400 |
Analysis date: | Wed Feb 24 21:00:00 CET 2016 |
Draw chromosome limits: | yes |
Summary
Globals
Reference size | 3,101,804,739 |
Number of reads | 912,383,669 |
Mapped reads | 894,970,438 / 98.09% |
Unmapped reads | 17,413,231 / 1.91% |
Paired reads | 894,970,438 / 98.09% |
Mapped reads, only first in pair | 447,733,402 / 49.07% |
Mapped reads, only second in pair | 447,237,036 / 49.02% |
Mapped reads, both in pair | 893,549,932 / 97.94% |
Mapped reads, singletons | 1,420,506 / 0.16% |
Read min/max/mean length | 30 / 151 / 150.37 |
Clipped reads | 64,443,293 / 7.06% |
Duplication rate | 23.24% |
ACGT Content
Number/percentage of A's | 38,959,134,016 / 29.51% |
Number/percentage of C's | 26,993,680,504 / 20.45% |
Number/percentage of T's | 39,160,075,074 / 29.66% |
Number/percentage of G's | 26,899,717,550 / 20.38% |
Number/percentage of N's | 0 / 0% |
GC Percentage | 40.82% |
Coverage
Mean | 42.59 |
Standard Deviation | 586.38 |
Mapping Quality
Mean Mapping Quality | 50.33 |
Insert size
Mean | 30,869.34 |
Standard Deviation | 1,742,379.2 |
P25/Median/P75 | 310 / 360 / 410 |
Mismatches and indels
General error rate | 0.78% |
Mismatches | 975,601,150 |
Insertions | 17,714,581 |
Deletions | 18,840,321 |
Homopolymer indels | 55.39% |
Chromosome stats
Name | Length | Mapped bases | Mean coverage | Standard deviation |
1 | 249250621 | 10829835549 | 43.45 | 1,247.98 |
2 | 243199373 | 11161883342 | 45.9 | 310.2 |
3 | 198022430 | 8670382898 | 43.78 | 26.96 |
4 | 191154276 | 8754923152 | 45.8 | 493.43 |
5 | 180915260 | 7909198671 | 43.72 | 20.33 |
6 | 171115067 | 7617397833 | 44.52 | 255.49 |
7 | 159138663 | 7038404925 | 44.23 | 219.93 |
8 | 146364022 | 6912993420 | 47.23 | 1,559.74 |
9 | 141213431 | 5448743936 | 38.59 | 261.79 |
10 | 135534747 | 6922783556 | 51.08 | 986.3 |
11 | 135006516 | 6010064473 | 44.52 | 222.78 |
12 | 133851895 | 5956087799 | 44.5 | 23.22 |
13 | 115169878 | 4211730206 | 36.57 | 18.52 |
14 | 107349540 | 4013206336 | 37.38 | 25.27 |
15 | 102531392 | 3765256168 | 36.72 | 23.79 |
16 | 90354753 | 4036095971 | 44.67 | 256.74 |
17 | 81195210 | 3664222313 | 45.13 | 153.61 |
18 | 78077248 | 3419973990 | 43.8 | 211.51 |
19 | 59128983 | 2670076347 | 45.16 | 586.83 |
20 | 63025520 | 2728397026 | 43.29 | 120.42 |
21 | 48129895 | 1770536627 | 36.79 | 191.22 |
22 | 51304566 | 1610779905 | 31.4 | 137.44 |
X | 155270560 | 3487018977 | 22.46 | 60.97 |
Y | 59373566 | 1395790021 | 23.51 | 557.66 |
MT | 16569 | 320070887 | 19,317.45 | 1,248.86 |
GL000207.1 | 4262 | 291699 | 68.44 | 75.51 |
GL000226.1 | 15008 | 247077641 | 16,463.06 | 13,113.08 |
GL000229.1 | 19913 | 3657176 | 183.66 | 91.42 |
GL000231.1 | 27386 | 5144728 | 187.86 | 108.6 |
GL000210.1 | 27682 | 559736 | 20.22 | 8.52 |
GL000239.1 | 33824 | 4041163 | 119.48 | 64.2 |
GL000235.1 | 34474 | 5891829 | 170.91 | 160.64 |
GL000201.1 | 36148 | 725673 | 20.08 | 11.41 |
GL000247.1 | 36422 | 2202668 | 60.48 | 32.37 |
GL000245.1 | 36651 | 4160944 | 113.53 | 59.46 |
GL000197.1 | 37175 | 795985 | 21.41 | 5.83 |
GL000203.1 | 37498 | 2390738 | 63.76 | 52.04 |
GL000246.1 | 38154 | 1107005 | 29.01 | 10.49 |
GL000249.1 | 38502 | 839925 | 21.82 | 6.06 |
GL000196.1 | 38914 | 854230 | 21.95 | 5.7 |
GL000248.1 | 39786 | 846965 | 21.29 | 9.81 |
GL000244.1 | 39929 | 1571445 | 39.36 | 19.61 |
GL000238.1 | 39939 | 978303 | 24.49 | 10 |
GL000202.1 | 40103 | 1240036 | 30.92 | 11.26 |
GL000234.1 | 40531 | 9358985 | 230.91 | 88.35 |
GL000232.1 | 40652 | 12651003 | 311.2 | 118.13 |
GL000206.1 | 41001 | 1046331 | 25.52 | 9.66 |
GL000240.1 | 41933 | 3093894 | 73.78 | 38.15 |
GL000236.1 | 41934 | 1504623 | 35.88 | 17.57 |
GL000241.1 | 42152 | 10231865 | 242.74 | 125.25 |
GL000243.1 | 43341 | 4076366 | 94.05 | 69.96 |
GL000242.1 | 43523 | 868084 | 19.95 | 8.81 |
GL000230.1 | 43691 | 3675379 | 84.12 | 30.06 |
GL000237.1 | 45867 | 6233371 | 135.9 | 58.7 |
GL000233.1 | 45941 | 4274411 | 93.04 | 35.85 |
GL000204.1 | 81310 | 2880132 | 35.42 | 13.82 |
GL000198.1 | 90085 | 14665260 | 162.79 | 192.38 |
GL000208.1 | 92689 | 22190039 | 239.4 | 673.39 |
GL000191.1 | 106433 | 2885910 | 27.11 | 11.75 |
GL000227.1 | 128374 | 2733197 | 21.29 | 12.82 |
GL000228.1 | 129120 | 44086331 | 341.44 | 2,224.98 |
GL000214.1 | 137718 | 31551743 | 229.1 | 190.35 |
GL000221.1 | 155397 | 19213720 | 123.64 | 69.95 |
GL000209.1 | 159169 | 3742819 | 23.51 | 6.5 |
GL000218.1 | 161147 | 16569047 | 102.82 | 35.1 |
GL000220.1 | 161802 | 363596212 | 2,247.17 | 3,221.15 |
GL000213.1 | 164239 | 3148975 | 19.17 | 8.6 |
GL000211.1 | 166566 | 9286160 | 55.75 | 22.79 |
GL000199.1 | 169874 | 376560032 | 2,216.7 | 5,438.65 |
GL000217.1 | 172149 | 12162312 | 70.65 | 41.56 |
GL000216.1 | 172294 | 99865872 | 579.62 | 3,041.97 |
GL000215.1 | 172545 | 3285175 | 19.04 | 9.12 |
GL000205.1 | 174588 | 27335397 | 156.57 | 83.93 |
GL000219.1 | 179198 | 24141646 | 134.72 | 113.49 |
GL000224.1 | 179693 | 43238362 | 240.62 | 407.6 |
GL000223.1 | 180455 | 4264924 | 23.63 | 7.5 |
GL000195.1 | 182896 | 31498117 | 172.22 | 56.82 |
GL000212.1 | 186858 | 80912410 | 433.02 | 5,800.21 |
GL000222.1 | 186861 | 12852518 | 68.78 | 244.39 |
GL000200.1 | 187035 | 2824280 | 15.1 | 7.24 |
GL000193.1 | 189789 | 21762533 | 114.67 | 62.17 |
GL000194.1 | 191469 | 22674523 | 118.42 | 60.41 |
GL000225.1 | 211173 | 106205977 | 502.93 | 1,259.43 |
GL000192.1 | 547496 | 23228432 | 42.43 | 21.23 |