BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR504701.sorted.bam
outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 517,802,328
number of mapped reads = 468,321,567 (90.44%)
number of supplementary alignments = 2,402,489 (0.46%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 236,082,132
number of mapped paired reads (second in pair) = 232,239,435
number of mapped paired reads (both in pair) = 460,704,842
number of mapped paired reads (singletons) = 7,616,725
number of mapped bases = 45,466,665,733 bp
number of sequenced bases = 45,457,023,687 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 115,196,186
duplication rate = 22.32%
>>>>>>> Insert size
mean insert size = 30,070.8572
std insert size = 1,647,802.6857
median insert size = 435
>>>>>>> Mapping quality
mean mapping quality = 53.9453
>>>>>>> ACTG content
number of A's = 12,075,540,856 bp (26.56%)
number of C's = 10,524,956,257 bp (23.15%)
number of T's = 12,041,955,853 bp (26.49%)
number of G's = 10,790,925,128 bp (23.74%)
number of N's = 23,645,593 bp (0.05%)
GC percentage = 46.89%
>>>>>>> Mismatches and indels
general error rate = 0.0076
number of mismatches = 337,180,837
number of insertions = 3,134,308
mapped reads with insertion percentage = 0.65%
number of deletions = 3,910,248
mapped reads with deletion percentage = 0.81%
homopolymer indels = 40.28%
>>>>>>> Coverage
mean coverageData = 14.6871X
std coverageData = 29.7329X
There is a 85.73% of reference with a coverageData >= 1X
There is a 80.37% of reference with a coverageData >= 2X
There is a 74.33% of reference with a coverageData >= 3X
There is a 68.71% of reference with a coverageData >= 4X
There is a 63.31% of reference with a coverageData >= 5X
There is a 58.36% of reference with a coverageData >= 6X
There is a 53.8% of reference with a coverageData >= 7X
There is a 49.66% of reference with a coverageData >= 8X
There is a 45.9% of reference with a coverageData >= 9X
There is a 42.5% of reference with a coverageData >= 10X
There is a 39.42% of reference with a coverageData >= 11X
There is a 36.62% of reference with a coverageData >= 12X
There is a 34.09% of reference with a coverageData >= 13X
There is a 31.79% of reference with a coverageData >= 14X
There is a 29.69% of reference with a coverageData >= 15X
There is a 27.78% of reference with a coverageData >= 16X
There is a 26.04% of reference with a coverageData >= 17X
There is a 24.44% of reference with a coverageData >= 18X
There is a 22.97% of reference with a coverageData >= 19X
There is a 21.63% of reference with a coverageData >= 20X
There is a 20.39% of reference with a coverageData >= 21X
There is a 19.25% of reference with a coverageData >= 22X
There is a 18.19% of reference with a coverageData >= 23X
There is a 17.22% of reference with a coverageData >= 24X
There is a 16.31% of reference with a coverageData >= 25X
There is a 15.48% of reference with a coverageData >= 26X
There is a 14.7% of reference with a coverageData >= 27X
There is a 13.97% of reference with a coverageData >= 28X
There is a 13.29% of reference with a coverageData >= 29X
There is a 12.66% of reference with a coverageData >= 30X
There is a 12.07% of reference with a coverageData >= 31X
There is a 11.51% of reference with a coverageData >= 32X
There is a 10.99% of reference with a coverageData >= 33X
There is a 10.51% of reference with a coverageData >= 34X
There is a 10.05% of reference with a coverageData >= 35X
There is a 9.62% of reference with a coverageData >= 36X
There is a 9.21% of reference with a coverageData >= 37X
There is a 8.83% of reference with a coverageData >= 38X
There is a 8.47% of reference with a coverageData >= 39X
There is a 8.13% of reference with a coverageData >= 40X
There is a 7.8% of reference with a coverageData >= 41X
There is a 7.5% of reference with a coverageData >= 42X
There is a 7.21% of reference with a coverageData >= 43X
There is a 6.94% of reference with a coverageData >= 44X
There is a 6.67% of reference with a coverageData >= 45X
There is a 6.43% of reference with a coverageData >= 46X
There is a 6.19% of reference with a coverageData >= 47X
There is a 5.97% of reference with a coverageData >= 48X
There is a 5.76% of reference with a coverageData >= 49X
There is a 5.55% of reference with a coverageData >= 50X
There is a 5.36% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 3983987119 15.983860353150334 31.839959158194976
chr2 243199373 3022033176 12.426155292760562 19.607078881491073
chr3 198022430 2571365835 12.985225133334643 19.328159698772573
chr4 191154276 2108114384 11.028340187378284 18.7090418484392
chr5 180915260 3126205344 17.279942797528523 25.984794714219742
chr6 171115067 1303372801 7.616937677381735 13.289187166277342
chr7 159138663 2151721628 13.52104879755085 20.065322745038753
chr8 146364022 2664703505 18.206000823071122 32.02533971485415
chr9 141213431 1238198879 8.768279831682582 18.29151395247812
chr10 135534747 2700777273 19.926825650104323 29.42363402013038
chr11 135006516 2601304738 19.267993983342254 32.07751814952962
chr12 133851895 2052157200 15.331551338888403 25.716238698638602
chr13 115169878 701270431 6.089009063637282 10.029598199653636
chr14 107349540 1281986139 11.942167046081426 18.235765807663565
chr15 102531392 1841206782 17.957493271914224 28.580838606333128
chr16 90354753 2179327526 24.119677755081682 36.625024748332066
chr17 81195210 1558617008 19.195923109257308 30.56280172222777
chr18 78077248 839841545 10.756546452559393 87.32044734894056
chr19 59128983 1891120767 31.982974694491194 47.089416405071944
chr20 63025520 1467404083 23.28269696148481 31.844540967091337
chr21 48129895 570780056 11.85915855415849 27.406011154259062
chr22 51304566 993986892 19.374238386501506 35.60393268722577
chrMT 16571 339720 20.500875022629895 8.098485666293815
chrX 155270560 2545181080 16.391910224320696 23.262957052988146
chrY 59373566 71661822 1.2069650995865735 41.63136811877385