BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR053616.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 6,780,602
number of mapped reads = 3,857,380 (56.89%)
number of supplementary alignments = 185 (0%)
number of secondary alignments = 0
number of mapped bases = 178,234,159 bp
number of sequenced bases = 178,194,581 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 553,974
duplication rate = 11.87%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.7756
>>>>>>> ACTG content
number of A's = 56,052,394 bp (31.46%)
number of C's = 33,559,512 bp (18.83%)
number of T's = 53,544,343 bp (30.05%)
number of G's = 35,034,226 bp (19.66%)
number of N's = 4,106 bp (0%)
GC percentage = 38.49%
>>>>>>> Mismatches and indels
general error rate = 0.0074
number of mismatches = 1,303,046
number of insertions = 9,030
mapped reads with insertion percentage = 0.23%
number of deletions = 27,590
mapped reads with deletion percentage = 0.71%
homopolymer indels = 45.71%
>>>>>>> Coverage
mean coverageData = 0.0576X
std coverageData = 0.425X
There is a 3.86% of reference with a coverageData >= 1X
There is a 1.03% of reference with a coverageData >= 2X
There is a 0.4% of reference with a coverageData >= 3X
There is a 0.19% of reference with a coverageData >= 4X
There is a 0.1% of reference with a coverageData >= 5X
There is a 0.05% of reference with a coverageData >= 6X
There is a 0.03% of reference with a coverageData >= 7X
There is a 0.02% of reference with a coverageData >= 8X
There is a 0.01% of reference with a coverageData >= 9X
There is a 0.01% of reference with a coverageData >= 10X
There is a 0.01% 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 13845418 0.05554817855398643 0.42609374834463165
chr2 243199373 15509519 0.06377285767097764 0.7228936186816265
chr3 198022430 12487007 0.063058548468474 0.38045080712790813
chr4 191154276 12352353 0.06461981002193223 0.3957101930342578
chr5 180915260 11376356 0.06288223558366497 0.3781555755353081
chr6 171115067 10777141 0.06298183549202012 0.4202911064024781
chr7 159138663 9720822 0.06108397429479472 0.4378916864459453
chr8 146364022 9235381 0.0630987101461314 0.432471635045181
chr9 141213431 7373262 0.05221360282649035 0.3691041620061139
chr10 135534747 8205049 0.06053834298299904 0.4028079809601391
chr11 135006516 8055495 0.05966745338424999 0.41658267360658574
chr12 133851895 8204679 0.061296696621291766 0.37618210530643764
chr13 115169878 6052614 0.052553793623016605 0.3493200513450731
chr14 107349540 5460702 0.0508684247738742 0.3671069833464758
chr15 102531392 5025441 0.04901368158544068 0.33210944725354735
chr16 90354753 4615974 0.051087229467607534 0.36548670720203014
chr17 81195210 4226129 0.05204899402316959 0.33898954426829286
chr18 78077248 4839131 0.061978759804648856 0.4378050284202588
chr19 59128983 2800907 0.0473694431713801 0.38878273077819137
chr20 63025520 3534151 0.056074920127592756 0.35936506815487784
chr21 48129895 2350523 0.048837068936053156 0.34951140285022997
chr22 51304566 1700519 0.03314556836909994 0.26176387595237005
chrMT 16571 70195 4.236014724518737 6.261204359331838
chrX 155270560 9960277 0.06414787838724868 0.407056095681144
chrY 59373566 455114 0.0076652630229418935 0.12706331920718117