BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716117.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 = 826,281 number of mapped reads = 649,227 (78.57%) number of supplementary alignments = 2,097 (0.25%) number of secondary alignments = 0 number of mapped bases = 36,741,702 bp number of sequenced bases = 36,730,438 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,168 duplication rate = 1.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3915 >>>>>>> ACTG content number of A's = 9,227,556 bp (25.12%) number of C's = 6,951,834 bp (18.93%) number of T's = 11,749,551 bp (31.99%) number of G's = 8,800,879 bp (23.96%) number of N's = 618 bp (0%) GC percentage = 42.89% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 191,538 number of insertions = 2,772 mapped reads with insertion percentage = 0.42% number of deletions = 7,155 mapped reads with deletion percentage = 1.09% homopolymer indels = 41.14% >>>>>>> Coverage mean coverageData = 0.0119X std coverageData = 0.132X There is a 1.12% of reference with a coverageData >= 1X There is a 0.05% 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 2935702 0.011778113082414346 0.1548189383301527 chr2 243199373 3072889 0.012635266950297605 0.18993931085727397 chr3 198022430 2370371 0.011970214687295777 0.1137464493872159 chr4 191154276 2551776 0.013349301168653951 0.12597392559599463 chr5 180915260 2162014 0.011950423640327522 0.11406827248262108 chr6 171115067 2069843 0.012096205414804297 0.1214019992490148 chr7 159138663 1986501 0.01248283077507067 0.1558274244883544 chr8 146364022 1875698 0.012815294184796315 0.12796691090571635 chr9 141213431 1492465 0.010568860124926785 0.11538443902663459 chr10 135534747 1759480 0.012981763266950282 0.13891901131817738 chr11 135006516 1610329 0.011927787248431772 0.12585930814229496 chr12 133851895 1654652 0.012361812285137988 0.11596850258965695 chr13 115169878 1144507 0.00993755502632381 0.10453665044476482 chr14 107349540 1104203 0.010286052460029171 0.10670788552848949 chr15 102531392 1048385 0.010225014793518067 0.1065485820141563 chr16 90354753 1103602 0.012214100125977878 0.12002186607193893 chr17 81195210 1048709 0.012915897378675417 0.1211455878246881 chr18 78077248 1014185 0.012989507519527328 0.15089461164981466 chr19 59128983 811034 0.013716352943192005 0.1495574674055245 chr20 63025520 836235 0.01326819675585382 0.1210559687494757 chr21 48129895 470302 0.009771515188221374 0.10725375726507898 chr22 51304566 466499 0.009092738451388518 0.09976925507909791 chrMT 16571 44366 2.6773278619274636 2.210229325334124 chrX 155270560 1998861 0.012873406265811111 0.12309676179967004 chrY 59373566 109094 0.0018374170081008777 0.058090391544661286