BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716269.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 = 810,634 number of mapped reads = 600,807 (74.12%) number of supplementary alignments = 671 (0.08%) number of secondary alignments = 0 number of mapped bases = 31,735,744 bp number of sequenced bases = 31,727,298 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,110 duplication rate = 4.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7246 >>>>>>> ACTG content number of A's = 6,936,715 bp (21.86%) number of C's = 5,890,807 bp (18.57%) number of T's = 10,285,380 bp (32.42%) number of G's = 8,613,756 bp (27.15%) number of N's = 640 bp (0%) GC percentage = 45.72% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 218,865 number of insertions = 1,761 mapped reads with insertion percentage = 0.29% number of deletions = 4,960 mapped reads with deletion percentage = 0.82% homopolymer indels = 41.35% >>>>>>> Coverage mean coverageData = 0.0103X std coverageData = 0.123X There is a 0.92% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 3114575 0.012495756229229214 0.14818447646227934 chr2 243199373 2753033 0.011320066191124597 0.17264378921663218 chr3 198022430 2127333 0.01074288907574763 0.11368195601265337 chr4 191154276 2041205 0.01067831200386017 0.11726413435212782 chr5 180915260 1941653 0.010732389296513737 0.11332100077279077 chr6 171115067 1385312 0.00809579205552951 0.10974770466258471 chr7 159138663 1845727 0.011598231160205235 0.1325082456438185 chr8 146364022 1983009 0.013548472998371143 0.13148214406915895 chr9 141213431 1393594 0.009868707177010662 0.11312434928053484 chr10 135534747 1660761 0.012253396540445823 0.13420923143981603 chr11 135006516 1351807 0.010012901895787015 0.11695286142088256 chr12 133851895 1502091 0.011222037611047644 0.11630937937305558 chr13 115169878 546370 0.0047440355888889625 0.07684199183289409 chr14 107349540 982907 0.00915613611385759 0.1049411601576484 chr15 102531392 624969 0.006095391741097205 0.08569330144525782 chr16 90354753 829411 0.009179494962484155 0.10989001736827028 chr17 81195210 1270700 0.0156499379704788 0.1434542026654103 chr18 78077248 819465 0.010495567159334305 0.12286202204701101 chr19 59128983 845690 0.01430246145109582 0.1466448439128322 chr20 63025520 825512 0.013098059325809609 0.12843689409645512 chr21 48129895 440070 0.009143381675775523 0.10893824230320621 chr22 51304566 352490 0.006870538579353737 0.09256103730248832 chrMT 16571 1051 0.06342405407036389 0.25200197982935063 chrX 155270560 1000333 0.006442515567664598 0.09036460610967632 chrY 59373566 96676 0.0016282666936326513 0.05448769508260777