BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR2971313.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 11,531,534
number of mapped reads = 10,681,774 (92.63%)
number of supplementary alignments = 2,044 (0.02%)
number of secondary alignments = 0
number of mapped bases = 510,768,747 bp
number of sequenced bases = 510,659,878 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,175,303
duplication rate = 8.94%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 33.1699
>>>>>>> ACTG content
number of A's = 140,906,131 bp (27.59%)
number of C's = 111,413,727 bp (21.82%)
number of T's = 144,079,896 bp (28.21%)
number of G's = 114,231,662 bp (22.37%)
number of N's = 28,462 bp (0.01%)
GC percentage = 44.19%
>>>>>>> Mismatches and indels
general error rate = 0.0055
number of mismatches = 2,772,481
number of insertions = 36,732
mapped reads with insertion percentage = 0.34%
number of deletions = 75,996
mapped reads with deletion percentage = 0.71%
homopolymer indels = 39.26%
>>>>>>> Coverage
mean coverageData = 0.165X
std coverageData = 1.4631X
There is a 10.98% of reference with a coverageData >= 1X
There is a 3.28% of reference with a coverageData >= 2X
There is a 1.07% of reference with a coverageData >= 3X
There is a 0.39% of reference with a coverageData >= 4X
There is a 0.16% of reference with a coverageData >= 5X
There is a 0.08% of reference with a coverageData >= 6X
There is a 0.05% of reference with a coverageData >= 7X
There is a 0.03% of reference with a coverageData >= 8X
There is a 0.02% of reference with a coverageData >= 9X
There is a 0.02% of reference with a coverageData >= 10X
There is a 0.01% of reference with a coverageData >= 11X
There is a 0.01% of reference with a coverageData >= 12X
There is a 0.01% of reference with a coverageData >= 13X
There is a 0.01% of reference with a coverageData >= 14X
There is a 0.01% of reference with a coverageData >= 15X
There is a 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0.01% of reference with a coverageData >= 19X
There is a 0.01% of reference with a coverageData >= 20X
There is a 0.01% 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% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% 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 40730437 0.16341157681609148 2.53750191477937
chr2 243199373 41794261 0.17185184519369628 1.4540610289458886
chr3 198022430 33944944 0.1714196922035549 0.5983148329033334
chr4 191154276 34408758 0.18000517027408794 0.9308693547521845
chr5 180915260 31486944 0.17404249923417184 0.6008075641111157
chr6 171115067 29511922 0.17246828416342788 0.6504124038143259
chr7 159138663 28911211 0.18167307965883817 2.0316699590025675
chr8 146364022 26289003 0.17961383296777675 2.6768965489683705
chr9 141213431 22255058 0.15759873435834867 1.5451307451973575
chr10 135534747 25113245 0.18529008653404577 1.7286156249404914
chr11 135006516 23137819 0.17138297976669511 1.203172616923035
chr12 133851895 24236357 0.1810684637673602 0.6631165087757024
chr13 115169878 15491050 0.13450609021223414 0.5132848778845173
chr14 107349540 15715089 0.14639176842304122 0.8046791837592149
chr15 102531392 14661652 0.14299671265557382 0.5564326383462597
chr16 90354753 14897229 0.16487487935471418 0.8071418685593503
chr17 81195210 14922740 0.18378842791342 0.8228669357320195
chr18 78077248 14592740 0.18690131086587478 2.979951792833076
chr19 59128983 12092841 0.20451630294402323 2.185283046643622
chr20 63025520 10549446 0.1673837201184536 0.6646265304647788
chr21 48129895 6648707 0.138140899746405 0.9079907183487229
chr22 51304566 6434650 0.12542061071133512 0.6397260226412631
chrMT 16571 119388 7.204634602619033 6.219922484747356
chrX 155270560 18322962 0.11800667170904774 0.6997318916062565
chrY 59373566 4500294 0.07579625586241527 0.8454386171631679