BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472727.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 17,489,628 number of mapped reads = 17,339,278 (99.14%) number of supplementary alignments = 59,789 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,695,148 number of mapped paired reads (second in pair) = 8,644,130 number of mapped paired reads (both in pair) = 17,253,614 number of mapped paired reads (singletons) = 85,664 number of mapped bases = 1,707,539,934 bp number of sequenced bases = 1,707,297,779 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,034,399 duplication rate = 47.48% >>>>>>> Insert size mean insert size = 22,589.3598 std insert size = 1,481,021.4343 median insert size = 230 >>>>>>> Mapping quality mean mapping quality = 55.4148 >>>>>>> ACTG content number of A's = 457,760,093 bp (26.81%) number of C's = 398,138,064 bp (23.32%) number of T's = 455,337,044 bp (26.67%) number of G's = 395,729,966 bp (23.18%) number of N's = 332,612 bp (0.02%) GC percentage = 46.5% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 9,973,062 number of insertions = 95,226 mapped reads with insertion percentage = 0.54% number of deletions = 97,768 mapped reads with deletion percentage = 0.56% homopolymer indels = 42.2% >>>>>>> Coverage mean coverageData = 0.5516X std coverageData = 18.4226X There is a 4.79% of reference with a coverageData >= 1X There is a 2.09% of reference with a coverageData >= 2X There is a 0.92% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 175217309 0.7029764190637664 24.953360943924633 chr2 243199373 125973403 0.5179840780263854 19.318858045095105 chr3 198022430 167575265 0.8462438573246475 18.682334328420602 chr4 191154276 67151252 0.35129348610543243 13.382702922687786 chr5 180915260 90970441 0.5028345370092053 17.919835974655825 chr6 171115067 98619293 0.5763331933826727 15.152143858349437 chr7 159138663 85411041 0.5367082982216584 23.835426060093894 chr8 146364022 96450932 0.6589797867128849 21.128784867272874 chr9 141213431 88968721 0.6300301633489805 15.698528965223407 chr10 135534747 43042382 0.3175745183631766 13.264576993887303 chr11 135006516 73595682 0.5451268885421797 15.61345691515082 chr12 133851895 92139120 0.6883661975797952 19.431120870145175 chr13 115169878 26939059 0.23390715930080258 8.1338888398336 chr14 107349540 44845228 0.417749605634081 14.411960703158131 chr15 102531392 43226587 0.42159368127958313 14.30567377121762 chr16 90354753 79984069 0.8852225958716305 26.735352838189872 chr17 81195210 54888795 0.6760102597185228 16.674221913451436 chr18 78077248 37888579 0.48527042090417943 20.596395225714954 chr19 59128983 49069200 0.8298671397747531 21.688784846584706 chr20 63025520 35213672 0.5587208483166819 18.884352517622432 chr21 48129895 6892773 0.1432118852534376 6.719634034748131 chr22 51304566 20508986 0.39974972208126663 11.985315401755074 chrMT 16571 2348 0.14169331965481866 0.4814203805101009 chrX 155270560 99688358 0.6420300023391428 21.74083677915681 chrY 59373566 3277439 0.05520030580612254 5.197907806471027