BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230407.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,556,879 number of mapped reads = 3,048,909 (85.72%) number of supplementary alignments = 34,906 (0.98%) number of secondary alignments = 0 number of mapped bases = 195,564,947 bp number of sequenced bases = 195,484,618 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 233,721 duplication rate = 6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1815 >>>>>>> ACTG content number of A's = 52,704,424 bp (26.96%) number of C's = 35,242,586 bp (18.03%) number of T's = 62,415,627 bp (31.93%) number of G's = 45,026,220 bp (23.03%) number of N's = 95,761 bp (0.05%) GC percentage = 41.06% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,709,462 number of insertions = 16,165 mapped reads with insertion percentage = 0.53% number of deletions = 49,486 mapped reads with deletion percentage = 1.61% homopolymer indels = 46.44% >>>>>>> Coverage mean coverageData = 0.0632X std coverageData = 0.5701X There is a 4.81% of reference with a coverageData >= 1X There is a 1.03% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 15112490 0.06063170450435909 0.918635148067771 chr2 243199373 16012078 0.06583930625511933 0.7227237975412928 chr3 198022430 11362627 0.05738050482463022 0.3017410511542525 chr4 191154276 13919277 0.0728169795165869 0.39512902001321304 chr5 180915260 14201693 0.07849914374276665 0.35341067972211593 chr6 171115067 11716783 0.06847312282558964 0.4188879024133603 chr7 159138663 11752298 0.0738494202379971 0.7647629827928388 chr8 146364022 9359973 0.06394995759272043 0.9577708573414323 chr9 141213431 8350842 0.05913631544013685 0.51904829180048 chr10 135534747 8186481 0.0604013449038275 0.49790508641639536 chr11 135006516 9201759 0.06815788802371583 0.5567320006529841 chr12 133851895 9205589 0.06877443909180367 0.3384640620333546 chr13 115169878 7016515 0.060923178194214986 0.3129362266275754 chr14 107349540 5771465 0.053763295119848675 0.32501128303655535 chr15 102531392 5613868 0.0547526751611838 0.30411044752003297 chr16 90354753 4559296 0.05045994647343013 0.3278547052724936 chr17 81195210 4488812 0.05528419718355307 0.3476887422669054 chr18 78077248 5759677 0.07376895507382637 0.9970602194645682 chr19 59128983 2943700 0.04978438408115357 0.6417631391927808 chr20 63025520 3617244 0.05739332257790178 0.3382345139551014 chr21 48129895 2566823 0.05333115727761301 0.3276680248721032 chr22 51304566 2146110 0.04183077973995531 0.25336393762054965 chrMT 16571 377265 22.766580170176816 18.217734313452393 chrX 155270560 11736832 0.07558955155439641 0.40787521869554205 chrY 59373566 585450 0.009860448671720342 0.2085282837913069