BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6238621.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,187,950
number of mapped reads = 2,630,083 (82.5%)
number of supplementary alignments = 23,378 (0.73%)
number of secondary alignments = 0
number of mapped bases = 159,713,702 bp
number of sequenced bases = 159,624,786 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,178,489
duplication rate = 22.66%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.707
>>>>>>> ACTG content
number of A's = 39,914,792 bp (25.01%)
number of C's = 26,967,945 bp (16.89%)
number of T's = 55,190,988 bp (34.58%)
number of G's = 37,547,543 bp (23.52%)
number of N's = 3,518 bp (0%)
GC percentage = 40.42%
>>>>>>> Mismatches and indels
general error rate = 0.0063
number of mismatches = 995,287
number of insertions = 10,502
mapped reads with insertion percentage = 0.4%
number of deletions = 52,479
mapped reads with deletion percentage = 1.97%
homopolymer indels = 41.38%
>>>>>>> Coverage
mean coverageData = 0.0516X
std coverageData = 1.107X
There is a 1.29% of reference with a coverageData >= 1X
There is a 0.71% of reference with a coverageData >= 2X
There is a 0.55% of reference with a coverageData >= 3X
There is a 0.45% of reference with a coverageData >= 4X
There is a 0.37% of reference with a coverageData >= 5X
There is a 0.3% of reference with a coverageData >= 6X
There is a 0.25% of reference with a coverageData >= 7X
There is a 0.2% of reference with a coverageData >= 8X
There is a 0.17% of reference with a coverageData >= 9X
There is a 0.14% of reference with a coverageData >= 10X
There is a 0.11% of reference with a coverageData >= 11X
There is a 0.09% of reference with a coverageData >= 12X
There is a 0.07% of reference with a coverageData >= 13X
There is a 0.06% of reference with a coverageData >= 14X
There is a 0.05% of reference with a coverageData >= 15X
There is a 0.04% of reference with a coverageData >= 16X
There is a 0.03% of reference with a coverageData >= 17X
There is a 0.03% of reference with a coverageData >= 18X
There is a 0.02% of reference with a coverageData >= 19X
There is a 0.02% of reference with a coverageData >= 20X
There is a 0.02% of reference with a coverageData >= 21X
There is a 0.01% of reference with a coverageData >= 22X
There is a 0.01% of reference with a coverageData >= 23X
There is a 0.01% of reference with a coverageData >= 24X
There is a 0.01% of reference with a coverageData >= 25X
There is a 0.01% of reference with a coverageData >= 26X
There is a 0.01% of reference with a coverageData >= 27X
There is a 0.01% of reference with a coverageData >= 28X
There is a 0.01% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 7569279 0.030368145000529406 0.6810547162565475
chr2 243199373 19542854 0.08035733710547024 2.276613324979715
chr3 198022430 15370486 0.07761992416717642 0.866692567297059
chr4 191154276 11109641 0.05811871558656632 0.7392509990145286
chr5 180915260 3712654 0.020521508246457484 0.43494594841714546
chr6 171115067 5047113 0.029495433035128343 0.9385822899235803
chr7 159138663 29079678 0.18273169732486694 1.677173118205205
chr8 146364022 5883217 0.04019578663942427 1.248540701505811
chr9 141213431 3698220 0.026188868677795952 0.5376393069196798
chr10 135534747 3774433 0.027848452766138267 0.5628268706214407
chr11 135006516 4010233 0.029703995916760047 0.5469803779934923
chr12 133851895 4472530 0.03341402077273542 0.5593932574828937
chr13 115169878 3992481 0.03466601744598531 0.7998343793576407
chr14 107349540 3234220 0.03012793534094324 0.5623803898739536
chr15 102531392 3147624 0.030699124810477554 0.6864612293045798
chr16 90354753 5311238 0.05878205433199513 0.7707601356480507
chr17 81195210 4205413 0.05179385581981991 0.6909698369873506
chr18 78077248 12904298 0.16527603534386867 3.07381189587859
chr19 59128983 1811896 0.030643111179503968 0.6554412822493367
chr20 63025520 1712095 0.027165107086780084 0.518781465155026
chr21 48129895 2380412 0.04945807590064346 0.6630248916376617
chr22 51304566 998213 0.019456611327732506 0.4311398686096426
chrMT 16571 45072 2.719932412045139 5.020088092344852
chrX 155270560 6275402 0.04041591657813304 0.6321875678421056
chrY 59373566 425000 0.007158067615477231 0.41700344747821205