BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1708616.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,059,607
number of mapped reads = 2,245,773 (73.4%)
number of supplementary alignments = 791 (0.03%)
number of secondary alignments = 0
number of mapped bases = 109,491,329 bp
number of sequenced bases = 109,470,617 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 77,805
duplication rate = 2.4%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.135
>>>>>>> ACTG content
number of A's = 32,372,701 bp (29.57%)
number of C's = 20,652,689 bp (18.87%)
number of T's = 34,486,445 bp (31.5%)
number of G's = 21,949,169 bp (20.05%)
number of N's = 9,613 bp (0.01%)
GC percentage = 38.92%
>>>>>>> Mismatches and indels
general error rate = 0.0064
number of mismatches = 695,290
number of insertions = 5,278
mapped reads with insertion percentage = 0.23%
number of deletions = 13,656
mapped reads with deletion percentage = 0.61%
homopolymer indels = 48.98%
>>>>>>> Coverage
mean coverageData = 0.0354X
std coverageData = 0.3682X
There is a 3.05% of reference with a coverageData >= 1X
There is a 0.36% of reference with a coverageData >= 2X
There is a 0.05% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% 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 8651656 0.03471066978806043 0.6645638924568997
chr2 243199373 9370667 0.0385308024622251 0.38181539348905413
chr3 198022430 7669789 0.03873192041931815 0.22345917121176373
chr4 191154276 6764994 0.03539023108224898 0.21723685833755088
chr5 180915260 7023155 0.03882013601284933 0.2295511114513495
chr6 171115067 6686375 0.03907531415687667 0.2923438677296494
chr7 159138663 6331602 0.03978669847188549 0.5351985431017836
chr8 146364022 5823277 0.03978625976812799 0.6656623017794581
chr9 141213431 4544020 0.0321783839385646 0.2843934292182548
chr10 135534747 5166784 0.038121471536741794 0.2901475149424403
chr11 135006516 4900749 0.03630009235998653 0.28483300113114524
chr12 133851895 4976034 0.03717567091597769 0.22717786195443238
chr13 115169878 3776116 0.03278735781937704 0.20694679871262966
chr14 107349540 3393198 0.031608873219205226 0.22399722609956407
chr15 102531392 2998581 0.029245491956258626 0.19403865695124295
chr16 90354753 2660109 0.029440720179933422 0.20974035082477666
chr17 81195210 2539645 0.03127826136541798 0.2313678424535602
chr18 78077248 3132445 0.04011981825998785 0.5799658738515644
chr19 59128983 1878814 0.031774840436541926 0.48880834008414437
chr20 63025520 2144286 0.03402250390000749 0.2156161649358688
chr21 48129895 1467057 0.030481200925121486 0.2106249131890304
chr22 51304566 1024072 0.019960640540259127 0.1586150667808975
chrMT 16571 1846 0.11139943274395027 0.32537530236774864
chrX 155270560 6306820 0.04061826015182788 0.2561317113742892
chrY 59373566 259238 0.004366219135296674 0.08474934754526943