BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472843.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 = 2,055,687 number of mapped reads = 1,686,166 (82.02%) number of supplementary alignments = 11,051 (0.54%) number of secondary alignments = 0 number of mapped bases = 108,209,272 bp number of sequenced bases = 108,165,310 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,297 duplication rate = 2.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1071 >>>>>>> ACTG content number of A's = 29,208,942 bp (27%) number of C's = 21,442,565 bp (19.82%) number of T's = 32,168,789 bp (29.74%) number of G's = 25,342,802 bp (23.43%) number of N's = 2,212 bp (0%) GC percentage = 43.25% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 856,721 number of insertions = 8,213 mapped reads with insertion percentage = 0.48% number of deletions = 24,670 mapped reads with deletion percentage = 1.45% homopolymer indels = 46.39% >>>>>>> Coverage mean coverageData = 0.035X std coverageData = 0.2482X There is a 3.09% of reference with a coverageData >= 1X There is a 0.31% 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% 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 8985570 0.03605034147537791 0.2680943794138293 chr2 243199373 9375620 0.03855116846867858 0.33812176376862674 chr3 198022430 8181949 0.041318294094259925 0.22453371203266229 chr4 191154276 6082050 0.03181749384460539 0.2021605793805111 chr5 180915260 4781286 0.026428317876557236 0.17959117465775856 chr6 171115067 5861613 0.034255387925599796 0.21752384083400395 chr7 159138663 7913931 0.049729781882106174 0.3382563986640376 chr8 146364022 5118498 0.034971012206811314 0.24102646284246182 chr9 141213431 4535784 0.032120060874379575 0.2527312733723097 chr10 135534747 4821524 0.03557408049760111 0.2316171745940657 chr11 135006516 4313233 0.0319483320345812 0.2442240713461739 chr12 133851895 4078669 0.03047150733278748 0.1926945214970281 chr13 115169878 4554947 0.03954981180061683 0.22801990453666318 chr14 107349540 2083603 0.019409519593656388 0.1635115911251019 chr15 102531392 3271190 0.03190427766746793 0.2070088936989278 chr16 90354753 3995444 0.044219522131835165 0.2506330087091709 chr17 81195210 2546756 0.03136584042334517 0.2036728563669949 chr18 78077248 2024277 0.02592659259711613 0.35503474182391054 chr19 59128983 2534874 0.04287024520614535 0.2573617814346254 chr20 63025520 4659364 0.07392821193700584 0.30929497463838523 chr21 48129895 1230712 0.02557063546471481 0.1905642451806302 chr22 51304566 1271542 0.024784187824530082 0.17997529169497037 chrMT 16571 196765 11.874057087683303 8.055812708587117 chrX 155270560 5343403 0.03441349731719909 0.21741583747063353 chrY 59373566 446668 0.007523011166282315 0.10678513285543258