BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716990.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 = 1,430,946 number of mapped reads = 1,219,828 (85.25%) number of supplementary alignments = 6,300 (0.44%) number of secondary alignments = 0 number of mapped bases = 68,841,563 bp number of sequenced bases = 68,823,215 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,612 duplication rate = 1.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.0815 >>>>>>> ACTG content number of A's = 16,583,391 bp (24.1%) number of C's = 13,705,290 bp (19.91%) number of T's = 21,309,967 bp (30.96%) number of G's = 17,224,013 bp (25.03%) number of N's = 554 bp (0%) GC percentage = 44.94% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 356,796 number of insertions = 5,517 mapped reads with insertion percentage = 0.45% number of deletions = 11,143 mapped reads with deletion percentage = 0.9% homopolymer indels = 38.32% >>>>>>> Coverage mean coverageData = 0.0222X std coverageData = 0.2279X There is a 2.07% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% 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 5541681 0.02223336887894855 0.3433413771143092 chr2 243199373 5646637 0.023218139629003074 0.3281585189324071 chr3 198022430 4443672 0.022440245784278074 0.1612944815595723 chr4 191154276 4308408 0.022538904648933933 0.18705879175362042 chr5 180915260 3969851 0.02194315172749938 0.15620398370676172 chr6 171115067 3872441 0.022630625507688344 0.1811208477511531 chr7 159138663 3833781 0.024090820720292214 0.28756879451103784 chr8 146364022 3359242 0.02295128238550318 0.21302531859758808 chr9 141213431 2859570 0.020249985994604154 0.19228841942893177 chr10 135534747 3439407 0.025376570039268232 0.306166034430593 chr11 135006516 3042068 0.022532749456329944 0.1931149695469618 chr12 133851895 3147010 0.023511135199094493 0.16350197162140215 chr13 115169878 2045308 0.017759053283012072 0.13979989556518976 chr14 107349540 2099453 0.019557168107101345 0.1595881079047886 chr15 102531392 2027456 0.019774002483063918 0.15337937502201723 chr16 90354753 2175184 0.02407381933742877 0.18303994367383214 chr17 81195210 2131981 0.02625747257750796 0.1795532429059721 chr18 78077248 1725241 0.02209659080197089 0.30173150712053903 chr19 59128983 1738786 0.029406661704294828 0.30014639353014855 chr20 63025520 1546137 0.02453191976837319 0.17439863305725525 chr21 48129895 879225 0.01826775229823377 0.16638919538823294 chr22 51304566 889536 0.017338339827297242 0.13993152981968243 chrMT 16571 19646 1.185565143926136 1.3443551191516059 chrX 155270560 3833236 0.024687461679793 0.18388636863693802 chrY 59373566 266606 0.004490314763980994 0.180502569963836