Input data and parameters
QualiMap command line
qualimap bamqc -bam /scratch/108823/ANALYSIS/P4107/piper_ngi/05_processed_alignments/P4107_1001.clean.dedup.bam -c -nw 400 -hm 3 |
Alignment
BAM file: | /scratch/108823/ANALYSIS/P4107/piper_ngi/05_processed_alignments/P4107_1001.clean.dedup.bam |
Program: | bwa (0.7.12-r1039) |
Size of a homopolymer: | 3 |
Number of windows: | 400 |
Analysis date: | Wed Feb 24 12:24:49 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 | 32,672,977,283 / 29.46% |
Number/percentage of C's | 22,732,803,038 / 20.5% |
Number/percentage of T's | 32,841,273,469 / 29.61% |
Number/percentage of G's | 22,647,323,821 / 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 | 50.32 |
Insert size
Mean | 28,931.62 |
Standard Deviation | 1,662,618.41 |
P25/Median/P75 | 306 / 355 / 406 |
Mismatches and indels
General error rate | 0.8% |
Mismatches | 836,121,400 |
Insertions | 14,847,635 |
Deletions | 15,566,029 |
Homopolymer indels | 55.48% |
Chromosome stats
Name | Length | Mapped bases | Mean coverage | Standard deviation |
1 | 249250621 | 9105489299 | 36.53 | 1,068 |
2 | 243199373 | 9356203228 | 38.47 | 243.97 |
3 | 198022430 | 7270434410 | 36.72 | 22.36 |
4 | 191154276 | 7330875123 | 38.35 | 417.4 |
5 | 180915260 | 6626088018 | 36.63 | 17.1 |
6 | 171115067 | 6390549766 | 37.35 | 217.37 |
7 | 159138663 | 5915360356 | 37.17 | 189.38 |
8 | 146364022 | 5786136214 | 39.53 | 1,261.57 |
9 | 141213431 | 4582291343 | 32.45 | 225.75 |
10 | 135534747 | 5828751978 | 43.01 | 840.04 |
11 | 135006516 | 5045932979 | 37.38 | 187.55 |
12 | 133851895 | 5004637861 | 37.39 | 19.58 |
13 | 115169878 | 3525257414 | 30.61 | 15.7 |
14 | 107349540 | 3372543297 | 31.42 | 21.18 |
15 | 102531392 | 3171432003 | 30.93 | 20.09 |
16 | 90354753 | 3408247021 | 37.72 | 215.83 |
17 | 81195210 | 3100340070 | 38.18 | 132.46 |
18 | 78077248 | 2870795677 | 36.77 | 181.19 |
19 | 59128983 | 2271955511 | 38.42 | 505.03 |
20 | 63025520 | 2300118661 | 36.5 | 103.18 |
21 | 48129895 | 1488010318 | 30.92 | 162.56 |
22 | 51304566 | 1367156875 | 26.65 | 117.18 |
X | 155270560 | 2919803745 | 18.8 | 51.56 |
Y | 59373566 | 1167393430 | 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 | 3159152 | 158.65 | 79.04 |
GL000231.1 | 27386 | 4327988 | 158.04 | 90.97 |
GL000210.1 | 27682 | 443325 | 16.01 | 7.04 |
GL000239.1 | 33824 | 3335009 | 98.6 | 51.47 |
GL000235.1 | 34474 | 4970708 | 144.19 | 145.48 |
GL000201.1 | 36148 | 604223 | 16.72 | 9.56 |
GL000247.1 | 36422 | 1806890 | 49.61 | 26.44 |
GL000245.1 | 36651 | 3592177 | 98.01 | 52.95 |
GL000197.1 | 37175 | 706090 | 18.99 | 5.22 |
GL000203.1 | 37498 | 1977250 | 52.73 | 43.64 |
GL000246.1 | 38154 | 941279 | 24.67 | 9.6 |
GL000249.1 | 38502 | 702256 | 18.24 | 5.08 |
GL000196.1 | 38914 | 724072 | 18.61 | 5.31 |
GL000248.1 | 39786 | 737561 | 18.54 | 8.09 |
GL000244.1 | 39929 | 1329653 | 33.3 | 17.02 |
GL000238.1 | 39939 | 836866 | 20.95 | 8.19 |
GL000202.1 | 40103 | 1027457 | 25.62 | 10.94 |
GL000234.1 | 40531 | 7957956 | 196.34 | 75.94 |
GL000232.1 | 40652 | 10564839 | 259.88 | 98.62 |
GL000206.1 | 41001 | 897988 | 21.9 | 8.87 |
GL000240.1 | 41933 | 2601987 | 62.05 | 32.89 |
GL000236.1 | 41934 | 1283507 | 30.61 | 14.9 |
GL000241.1 | 42152 | 8544943 | 202.72 | 107.75 |
GL000243.1 | 43341 | 3449413 | 79.59 | 57.86 |
GL000242.1 | 43523 | 715964 | 16.45 | 7.41 |
GL000230.1 | 43691 | 3039321 | 69.56 | 24.01 |
GL000237.1 | 45867 | 5240203 | 114.25 | 50.83 |
GL000233.1 | 45941 | 3575976 | 77.84 | 29.99 |
GL000204.1 | 81310 | 2332875 | 28.69 | 11.79 |
GL000198.1 | 90085 | 12126545 | 134.61 | 160.15 |
GL000208.1 | 92689 | 18765909 | 202.46 | 566.6 |
GL000191.1 | 106433 | 2428145 | 22.81 | 9.94 |
GL000227.1 | 128374 | 2343658 | 18.26 | 10.99 |
GL000228.1 | 129120 | 38935453 | 301.54 | 1,968.31 |
GL000214.1 | 137718 | 26470572 | 192.21 | 159.84 |
GL000221.1 | 155397 | 16047366 | 103.27 | 58.29 |
GL000209.1 | 159169 | 3117201 | 19.58 | 5.86 |
GL000218.1 | 161147 | 13934690 | 86.47 | 29.67 |
GL000220.1 | 161802 | 311220342 | 1,923.46 | 2,724.93 |
GL000213.1 | 164239 | 2571587 | 15.66 | 7.2 |
GL000211.1 | 166566 | 7725792 | 46.38 | 18.79 |
GL000199.1 | 169874 | 318433197 | 1,874.53 | 4,623.22 |
GL000217.1 | 172149 | 10058658 | 58.43 | 34.62 |
GL000216.1 | 172294 | 86085999 | 499.65 | 2,629.95 |
GL000215.1 | 172545 | 2711180 | 15.71 | 7.61 |
GL000205.1 | 174588 | 23087486 | 132.24 | 71.54 |
GL000219.1 | 179198 | 20347063 | 113.55 | 95.89 |
GL000224.1 | 179693 | 36547985 | 203.39 | 344.46 |
GL000223.1 | 180455 | 3575782 | 19.82 | 6.48 |
GL000195.1 | 182896 | 26580346 | 145.33 | 47.36 |
GL000212.1 | 186858 | 68692613 | 367.62 | 4,950.42 |
GL000222.1 | 186861 | 10997539 | 58.85 | 217.34 |
GL000200.1 | 187035 | 2371917 | 12.68 | 6.49 |
GL000193.1 | 189789 | 18259299 | 96.21 | 53.02 |
GL000194.1 | 191469 | 19046981 | 99.48 | 50.29 |
GL000225.1 | 211173 | 93650597 | 443.48 | 1,123.8 |
GL000192.1 | 547496 | 19491534 | 35.6 | 18.17 |