BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536755.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 23,565,000 number of mapped reads = 22,720,707 (96.42%) number of supplementary alignments = 552 (0%) number of secondary alignments = 0 number of mapped bases = 1,133,082,026 bp number of sequenced bases = 1,132,985,828 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 207,477 duplication rate = 0.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5912 >>>>>>> ACTG content number of A's = 353,216,851 bp (31.18%) number of C's = 211,421,810 bp (18.66%) number of T's = 352,944,678 bp (31.15%) number of G's = 214,922,542 bp (18.97%) number of N's = 479,947 bp (0.04%) GC percentage = 37.63% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 3,964,998 number of insertions = 63,168 mapped reads with insertion percentage = 0.28% number of deletions = 58,578 mapped reads with deletion percentage = 0.26% homopolymer indels = 48.36% >>>>>>> Coverage mean coverageData = 0.366X std coverageData = 0.6762X There is a 27.84% of reference with a coverageData >= 1X There is a 6.87% of reference with a coverageData >= 2X There is a 1.5% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.01% 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 88635174 0.3556066325708372 0.6808384860804214 chr2 243199373 103011454 0.42356792589263786 0.7116523183659795 chr3 198022430 88000049 0.4443943496703883 0.7256924862283926 chr4 191154276 95608206 0.5001625284071595 0.7670572660919649 chr5 180915260 80375038 0.44426897985277747 0.7254374362094917 chr6 171115067 76576807 0.4475164480986353 0.7321936385432909 chr7 159138663 64743508 0.4068370739045357 0.709000163335071 chr8 146364022 64179455 0.438492015476317 0.7248221124197137 chr9 141213431 47082814 0.33341597655820715 0.651819094335203 chr10 135534747 48891216 0.3607282787785777 0.6591625791390859 chr11 135006516 51197993 0.3792260886133822 0.6886839638754633 chr12 133851895 52866034 0.39495917484022175 0.7012118856078974 chr13 115169878 48073102 0.4174103753066405 0.7234821786154264 chr14 107349540 37155993 0.3461215856164824 0.6695610394277767 chr15 102531392 29625007 0.28893596802040883 0.6100704218139879 chr16 90354753 20561130 0.22756002664298136 0.535054490126125 chr17 81195210 17307953 0.21316470515933145 0.5212991788803323 chr18 78077248 33954925 0.4348888552014538 0.7227782816706748 chr19 59128983 7569359 0.12801436141731035 0.39084918684224035 chr20 63025520 16906988 0.268256223828062 0.5793629362350569 chr21 48129895 14986115 0.31136812162170724 0.6545860524222595 chr22 51304566 5625306 0.1096453286438482 0.36974065975083314 chrMT 16571 504 0.03041457968740571 0.20147771209560125 chrX 155270560 34999494 0.22540972351745237 0.5002161325462505 chrY 59373566 5148402 0.08671202265331343 0.33143171220627543