BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867850.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 = 12,486,163 number of mapped reads = 12,115,797 (97.03%) number of supplementary alignments = 47,552 (0.38%) number of secondary alignments = 0 number of mapped bases = 1,081,814,218 bp number of sequenced bases = 1,081,537,869 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 621,859 duplication rate = 1.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.4213 >>>>>>> ACTG content number of A's = 307,245,119 bp (28.41%) number of C's = 230,094,550 bp (21.27%) number of T's = 309,459,808 bp (28.61%) number of G's = 234,251,528 bp (21.66%) number of N's = 486,864 bp (0.05%) GC percentage = 42.93% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 4,728,816 number of insertions = 104,185 mapped reads with insertion percentage = 0.84% number of deletions = 112,795 mapped reads with deletion percentage = 0.91% homopolymer indels = 35.88% >>>>>>> Coverage mean coverageData = 0.3495X std coverageData = 5.7837X There is a 26.93% of reference with a coverageData >= 1X There is a 5.17% of reference with a coverageData >= 2X There is a 0.85% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 103379593 0.41476162661195537 9.225666815275167 chr2 243199373 93527797 0.3845725251931468 2.299672496470909 chr3 198022430 73534887 0.3713462510282295 4.3908391599384595 chr4 191154276 57946518 0.30314005635950303 2.581575241385755 chr5 180915260 50227273 0.27762872518327086 0.6343181931892231 chr6 171115067 78011473 0.4559006659536299 2.2933475373952317 chr7 159138663 61529056 0.3866380101484201 3.3382114520308104 chr8 146364022 68090867 0.4652158779840035 1.654632711617628 chr9 141213431 43011908 0.3045879396556833 2.087598522572655 chr10 135534747 70445973 0.5197631940095775 22.162979750248894 chr11 135006516 40975546 0.3035079136476642 1.5001894568805825 chr12 133851895 47579946 0.3554671078806916 0.698503847914467 chr13 115169878 27116263 0.23544579078220434 0.5132975581728385 chr14 107349540 27843509 0.2593724109111227 0.6987062102745618 chr15 102531392 31763155 0.30978956181537065 0.5961913367937551 chr16 90354753 30077825 0.3328859191281282 3.3206520283334693 chr17 81195210 27601398 0.33993874761824006 1.19819230013079 chr18 78077248 23971672 0.3070250631784563 3.915201815369212 chr19 59128983 21975267 0.3716496696721471 5.196016382865755 chr20 63025520 20107535 0.3190379865172076 0.9202300424514607 chr21 48129895 12569275 0.2611531772508542 1.898628769748503 chr22 51304566 17702760 0.34505232926051843 0.6957153596147978 chrMT 16571 1677929 101.25695492124797 34.627762904197716 chrX 155270560 47071270 0.3031564386706662 1.041369672982804 chrY 59373566 4075523 0.06864204518219438 3.187597424802737