BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472736.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 12,438,598
number of mapped reads = 12,317,897 (99.03%)
number of supplementary alignments = 39,898 (0.32%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 6,181,700
number of mapped paired reads (second in pair) = 6,136,197
number of mapped paired reads (both in pair) = 12,247,758
number of mapped paired reads (singletons) = 70,139
number of mapped bases = 1,212,460,822 bp
number of sequenced bases = 1,212,300,530 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 7,397,171
duplication rate = 45.66%
>>>>>>> Insert size
mean insert size = 20,906.9283
std insert size = 1,454,598.8774
median insert size = 232
>>>>>>> Mapping quality
mean mapping quality = 55.13
>>>>>>> ACTG content
number of A's = 323,629,673 bp (26.7%)
number of C's = 284,102,237 bp (23.43%)
number of T's = 322,092,674 bp (26.57%)
number of G's = 282,237,796 bp (23.28%)
number of N's = 238,150 bp (0.02%)
GC percentage = 46.72%
>>>>>>> Mismatches and indels
general error rate = 0.0061
number of mismatches = 7,290,663
number of insertions = 69,167
mapped reads with insertion percentage = 0.56%
number of deletions = 65,559
mapped reads with deletion percentage = 0.52%
homopolymer indels = 45.14%
>>>>>>> Coverage
mean coverageData = 0.3917X
std coverageData = 14.4613X
There is a 3.51% of reference with a coverageData >= 1X
There is a 1.54% of reference with a coverageData >= 2X
There is a 0.72% of reference with a coverageData >= 3X
There is a 0.54% of reference with a coverageData >= 4X
There is a 0.43% of reference with a coverageData >= 5X
There is a 0.39% of reference with a coverageData >= 6X
There is a 0.35% of reference with a coverageData >= 7X
There is a 0.33% of reference with a coverageData >= 8X
There is a 0.32% of reference with a coverageData >= 9X
There is a 0.3% of reference with a coverageData >= 10X
There is a 0.29% of reference with a coverageData >= 11X
There is a 0.28% of reference with a coverageData >= 12X
There is a 0.27% of reference with a coverageData >= 13X
There is a 0.26% of reference with a coverageData >= 14X
There is a 0.25% of reference with a coverageData >= 15X
There is a 0.25% of reference with a coverageData >= 16X
There is a 0.24% of reference with a coverageData >= 17X
There is a 0.23% of reference with a coverageData >= 18X
There is a 0.23% of reference with a coverageData >= 19X
There is a 0.22% of reference with a coverageData >= 20X
There is a 0.22% of reference with a coverageData >= 21X
There is a 0.21% of reference with a coverageData >= 22X
There is a 0.21% of reference with a coverageData >= 23X
There is a 0.2% of reference with a coverageData >= 24X
There is a 0.2% of reference with a coverageData >= 25X
There is a 0.19% of reference with a coverageData >= 26X
There is a 0.19% of reference with a coverageData >= 27X
There is a 0.19% of reference with a coverageData >= 28X
There is a 0.18% of reference with a coverageData >= 29X
There is a 0.18% of reference with a coverageData >= 30X
There is a 0.18% of reference with a coverageData >= 31X
There is a 0.17% of reference with a coverageData >= 32X
There is a 0.17% of reference with a coverageData >= 33X
There is a 0.17% of reference with a coverageData >= 34X
There is a 0.17% of reference with a coverageData >= 35X
There is a 0.16% of reference with a coverageData >= 36X
There is a 0.16% of reference with a coverageData >= 37X
There is a 0.16% of reference with a coverageData >= 38X
There is a 0.16% of reference with a coverageData >= 39X
There is a 0.15% of reference with a coverageData >= 40X
There is a 0.15% of reference with a coverageData >= 41X
There is a 0.15% of reference with a coverageData >= 42X
There is a 0.15% of reference with a coverageData >= 43X
There is a 0.14% of reference with a coverageData >= 44X
There is a 0.14% of reference with a coverageData >= 45X
There is a 0.14% of reference with a coverageData >= 46X
There is a 0.14% of reference with a coverageData >= 47X
There is a 0.14% of reference with a coverageData >= 48X
There is a 0.14% of reference with a coverageData >= 49X
There is a 0.13% of reference with a coverageData >= 50X
There is a 0.13% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 147116158 0.5902338674614576 20.142424119901097
chr2 243199373 74731371 0.3072843900794103 16.468186260965428
chr3 198022430 116201550 0.5868100396505588 13.992289860693246
chr4 191154276 72256530 0.37800111779869366 17.160496773309397
chr5 180915260 56842440 0.3141937280470426 12.181119672841504
chr6 171115067 74779786 0.43701462010940273 13.831223295262406
chr7 159138663 51901932 0.32614281797755207 9.713576367493554
chr8 146364022 52516093 0.3588046589755507 10.488385009389827
chr9 141213431 76235764 0.539861990889521 16.77706982021435
chr10 135534747 31817383 0.23475443533310317 8.645512151221228
chr11 135006516 74061499 0.5485772183025596 25.317737628731244
chr12 133851895 52537312 0.3925033112157284 12.051581723939151
chr13 115169878 23972285 0.20814717716380668 10.485903561984864
chr14 107349540 32533560 0.3030619413925761 10.114261036594453
chr15 102531392 28782151 0.2807155002830743 10.039238002441044
chr16 90354753 38026931 0.42086254167503506 12.871689887599713
chr17 81195210 39565897 0.48729348689411606 11.032055615523397
chr18 78077248 25529558 0.32697819984638804 14.76524043278517
chr19 59128983 23880539 0.4038719725654676 10.290503789602093
chr20 63025520 21400121 0.3395469168679608 9.672854908691711
chr21 48129895 6634788 0.13785170318780043 7.809729801969763
chr22 51304566 14108992 0.27500460680244326 9.56511516578719
chrMT 16571 1264 0.07627783477158892 0.3225090984321578
chrX 155270560 75304450 0.48498859023887075 16.62593953547365
chrY 59373566 1722468 0.02901068802234314 1.2848830457985412