BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716855.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,574,701 number of mapped reads = 2,400,724 (93.24%) number of supplementary alignments = 50,826 (1.97%) number of secondary alignments = 0 number of mapped bases = 185,083,368 bp number of sequenced bases = 185,011,288 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 150,331 duplication rate = 4.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1272 >>>>>>> ACTG content number of A's = 45,998,911 bp (24.86%) number of C's = 36,527,032 bp (19.74%) number of T's = 54,961,905 bp (29.71%) number of G's = 47,516,575 bp (25.68%) number of N's = 6,865 bp (0%) GC percentage = 45.43% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,214,246 number of insertions = 15,839 mapped reads with insertion percentage = 0.65% number of deletions = 34,546 mapped reads with deletion percentage = 1.41% homopolymer indels = 38.44% >>>>>>> Coverage mean coverageData = 0.0598X std coverageData = 0.4739X There is a 4.68% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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 18708664 0.0750596484973251 0.8631836387766328 chr2 243199373 17730988 0.07290721099021913 0.5421661340723652 chr3 198022430 12073737 0.06097156266590608 0.3093337020366105 chr4 191154276 9292144 0.04861070437158309 0.43356578415166186 chr5 180915260 9711004 0.05367708616730286 0.290222013934424 chr6 171115067 11513331 0.06728414511855932 0.3459023579567328 chr7 159138663 11938872 0.07502181917916452 0.6430379083019705 chr8 146364022 11690719 0.07987426718842149 0.5025748027542283 chr9 141213431 5537430 0.0392131963708183 0.32259040160501423 chr10 135534747 9745032 0.07190061748519735 0.6949466425332594 chr11 135006516 5736817 0.042492889750595446 0.3702118606392786 chr12 133851895 6260206 0.04676964790076375 0.2680048143744271 chr13 115169878 3597239 0.031234199970238748 0.2140065341832173 chr14 107349540 3596475 0.033502472390659524 0.24743013628541227 chr15 102531392 3776786 0.03683541134406914 0.23404911170868742 chr16 90354753 5842003 0.06465628875107433 0.3467437630018418 chr17 81195210 4866939 0.05994120835453225 0.3491907069260757 chr18 78077248 5537901 0.07092848610647752 0.5321672110547382 chr19 59128983 4289204 0.07253978983538412 0.6462105284116474 chr20 63025520 5121472 0.08126028948273652 0.380254841943771 chr21 48129895 2910133 0.06046414603647068 0.3898503265701396 chr22 51304566 2848084 0.055513265622400935 0.2982036274824349 chrMT 16571 44616 2.6924144589946293 2.718991670724515 chrX 155270560 12055590 0.0776424713094356 0.3654615550488422 chrY 59373566 657982 0.01108206975474574 0.3797846291804945