BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236121.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 = 3,141,365 number of mapped reads = 2,744,383 (87.36%) number of supplementary alignments = 30,604 (0.97%) number of secondary alignments = 0 number of mapped bases = 181,177,110 bp number of sequenced bases = 181,083,618 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 263,539 duplication rate = 7.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0179 >>>>>>> ACTG content number of A's = 50,964,120 bp (28.14%) number of C's = 32,859,826 bp (18.15%) number of T's = 57,902,142 bp (31.98%) number of G's = 39,355,775 bp (21.73%) number of N's = 1,755 bp (0%) GC percentage = 39.88% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,365,715 number of insertions = 13,901 mapped reads with insertion percentage = 0.5% number of deletions = 53,558 mapped reads with deletion percentage = 1.93% homopolymer indels = 46.52% >>>>>>> Coverage mean coverageData = 0.0585X std coverageData = 0.6534X There is a 3.78% of reference with a coverageData >= 1X There is a 1.26% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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 19913008 0.07989150807371509 1.340034852273332 chr2 243199373 6112018 0.02513171775323615 0.5335983204782322 chr3 198022430 9770466 0.04934019848155585 0.3139138873403607 chr4 191154276 7255815 0.03795790055985983 0.3595547462397742 chr5 180915260 10133597 0.05601294771928029 0.3395286932940727 chr6 171115067 20538832 0.120029360126423 0.6391444032950637 chr7 159138663 14360945 0.09024170952096035 1.0679837472094773 chr8 146364022 15764626 0.10770834105665666 1.0467910921186419 chr9 141213431 5865745 0.04153815227391508 0.47259868991070864 chr10 135534747 8054771 0.0594295645824314 0.5520301617875822 chr11 135006516 4573799 0.03387835739720889 0.3635120484504254 chr12 133851895 3844007 0.028718360692614773 0.2532185123778438 chr13 115169878 10011882 0.08693142837226936 0.4260410574334233 chr14 107349540 3285368 0.0306043975595983 0.2684252344837343 chr15 102531392 6203641 0.06050479642371382 0.35229599073934437 chr16 90354753 4729740 0.05234633312538633 0.35657066098476203 chr17 81195210 6264050 0.0771480238797338 0.4908417505111461 chr18 78077248 4879728 0.062498719217152734 0.9509589482402953 chr19 59128983 4339416 0.0733889842143911 0.8645110059282429 chr20 63025520 2348087 0.0372561305325208 0.28247000439142733 chr21 48129895 3724299 0.07738016050107735 0.4325717664431724 chr22 51304566 2066444 0.0402779744789187 0.2739755956743488 chrMT 16571 157205 9.486753967775028 6.993522446563885 chrX 155270560 6558827 0.04224127870730936 0.31599559607539257 chrY 59373566 420794 0.007087228009852061 0.239379207964659