BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3080811.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,044,821
number of mapped reads = 2,786,869 (91.53%)
number of supplementary alignments = 25,999 (0.85%)
number of secondary alignments = 0
number of mapped bases = 189,613,488 bp
number of sequenced bases = 189,544,046 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 205,820
duplication rate = 6.15%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.8224
>>>>>>> ACTG content
number of A's = 54,108,711 bp (28.55%)
number of C's = 35,245,476 bp (18.59%)
number of T's = 59,978,455 bp (31.64%)
number of G's = 40,185,082 bp (21.2%)
number of N's = 26,322 bp (0.01%)
GC percentage = 39.8%
>>>>>>> Mismatches and indels
general error rate = 0.0083
number of mismatches = 1,549,430
number of insertions = 14,074
mapped reads with insertion percentage = 0.5%
number of deletions = 39,259
mapped reads with deletion percentage = 1.4%
homopolymer indels = 48.82%
>>>>>>> Coverage
mean coverageData = 0.0613X
std coverageData = 0.4537X
There is a 4.4% of reference with a coverageData >= 1X
There is a 1.17% of reference with a coverageData >= 2X
There is a 0.33% of reference with a coverageData >= 3X
There is a 0.1% of reference with a coverageData >= 4X
There is a 0.03% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% 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 14945482 0.059961664047368614 0.698869477014948
chr2 243199373 15544994 0.06391872564572772 0.4887705400528348
chr3 198022430 13043016 0.06586635665464766 0.3354645933419533
chr4 191154276 13336673 0.06976915860359828 0.3652339094422652
chr5 180915260 11645265 0.06436861655561836 0.3317864682186382
chr6 171115067 11049131 0.0645713506923385 0.4368342395601422
chr7 159138663 11002251 0.06913625383417982 0.5341414174212662
chr8 146364022 9478738 0.06476139334296238 0.7243423732518725
chr9 141213431 7844409 0.05555002059258797 0.4035361780740052
chr10 135534747 8907718 0.06572276259164744 0.4433891585530322
chr11 135006516 7864723 0.058254395661910124 0.355769224514842
chr12 133851895 8725806 0.06519000720908733 0.3391545489861054
chr13 115169878 6194039 0.05378176227641745 0.30377861289893715
chr14 107349540 5944097 0.05537142497303668 0.32261038843387807
chr15 102531392 5211215 0.05082555594290576 0.29457102735675383
chr16 90354753 5246795 0.05806883230592197 0.34973960851906416
chr17 81195210 5133109 0.06321935739805341 0.33650769114187984
chr18 78077248 5073765 0.06498391183049894 0.7479953977449832
chr19 59128983 3438598 0.05815418810771699 0.5059242261013965
chr20 63025520 3724554 0.059095966205435516 0.3265756521859635
chr21 48129895 2552547 0.05303454329164857 0.3200381901251164
chr22 51304566 1862905 0.036310705756676706 0.24718097245807485
chrMT 16571 239472 14.451270291473055 7.884245704666936
chrX 155270560 11118144 0.07160497134807783 0.366336232485348
chrY 59373566 486042 0.008186168235204199 0.20451552987117103