BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237847.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 = 3,332,505 number of mapped reads = 2,971,238 (89.16%) number of supplementary alignments = 20,778 (0.62%) number of secondary alignments = 0 number of mapped bases = 193,427,846 bp number of sequenced bases = 193,323,186 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,411 duplication rate = 2.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3122 >>>>>>> ACTG content number of A's = 53,857,583 bp (27.86%) number of C's = 38,170,251 bp (19.74%) number of T's = 57,333,942 bp (29.66%) number of G's = 43,781,151 bp (22.65%) number of N's = 180,259 bp (0.09%) GC percentage = 42.39% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,595,930 number of insertions = 15,773 mapped reads with insertion percentage = 0.53% number of deletions = 61,580 mapped reads with deletion percentage = 2.05% homopolymer indels = 43.91% >>>>>>> Coverage mean coverageData = 0.0625X std coverageData = 0.6613X There is a 5.31% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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% 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 22820424 0.09155613698551227 1.3604078969096398 chr2 243199373 22474310 0.09241105239198129 0.5592156597632526 chr3 198022430 14489078 0.07316887283930411 0.3835249834954815 chr4 191154276 7074836 0.03701113126028109 0.29369021074799945 chr5 180915260 7808280 0.043159874960243816 0.2338912284700422 chr6 171115067 9430006 0.055109150616175724 0.3229851581715138 chr7 159138663 14686498 0.09228742860558029 1.3683811797507355 chr8 146364022 9191082 0.0627960469684278 0.42319067403975935 chr9 141213431 10095031 0.07148775388086137 0.4706330965642126 chr10 135534747 10574172 0.07801816312093016 1.240450526852298 chr11 135006516 9408820 0.0696915991817758 0.3639947521775543 chr12 133851895 9106935 0.06803740059115337 0.30145718137338695 chr13 115169878 4774235 0.041453851327340994 0.22395339958724192 chr14 107349540 2347770 0.021870331256193552 0.2388201333792852 chr15 102531392 3405348 0.03321273547129839 0.20120031666964883 chr16 90354753 4656662 0.05153754335424944 0.3525616487666756 chr17 81195210 2944297 0.03626195436898309 0.25644387226625265 chr18 78077248 2861057 0.036643927306454244 0.6141837103978199 chr19 59128983 3357684 0.056785755980277894 0.8769109616760928 chr20 63025520 3929500 0.062347760081947756 0.28888126066992226 chr21 48129895 2261311 0.04698350162617226 0.30962962211734535 chr22 51304566 1127806 0.0219825658402412 0.16737040406469408 chrMT 16571 110651 6.677388208315732 4.264443341763491 chrX 155270560 13924123 0.08967651691344451 0.39286581800573683 chrY 59373566 567930 0.009565367860842314 0.24794571493369738