BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716928.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 = 1,028,948 number of mapped reads = 926,216 (90.02%) number of supplementary alignments = 4,812 (0.47%) number of secondary alignments = 0 number of mapped bases = 53,794,518 bp number of sequenced bases = 53,778,721 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,769 duplication rate = 1.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6583 >>>>>>> ACTG content number of A's = 13,067,004 bp (24.3%) number of C's = 9,695,720 bp (18.03%) number of T's = 17,609,240 bp (32.74%) number of G's = 13,405,357 bp (24.93%) number of N's = 1,400 bp (0%) GC percentage = 42.96% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 270,201 number of insertions = 3,725 mapped reads with insertion percentage = 0.4% number of deletions = 9,853 mapped reads with deletion percentage = 1.06% homopolymer indels = 41.71% >>>>>>> Coverage mean coverageData = 0.0174X std coverageData = 0.1863X There is a 1.62% 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% 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 5777575 0.02317978176672226 0.3292705581280601 chr2 243199373 4907283 0.02017802488331251 0.22703141556926432 chr3 198022430 4860113 0.024543244924324987 0.1664957152598556 chr4 191154276 2584071 0.01351824847486017 0.12599210638597555 chr5 180915260 2467551 0.013639264039970978 0.12349310371694484 chr6 171115067 3854076 0.022523300066849168 0.2091236445734805 chr7 159138663 3189851 0.020044475301391716 0.2192689292892063 chr8 146364022 3854985 0.026338337436504718 0.18766824608543461 chr9 141213431 1357288 0.009611606986590391 0.12998807055397552 chr10 135534747 2721033 0.02007627608586601 0.20146286555435153 chr11 135006516 1816527 0.013455106122433379 0.1521066764587794 chr12 133851895 2433265 0.01817878633694353 0.14312478987108826 chr13 115169878 1352850 0.011746561023534295 0.11479812468975216 chr14 107349540 1212525 0.011295111278539247 0.11755434678477772 chr15 102531392 1636209 0.015958127243605548 0.13327911064222855 chr16 90354753 1163977 0.012882299617375966 0.13165760578980074 chr17 81195210 1231950 0.015172693068963058 0.132435180793052 chr18 78077248 1083187 0.013873273299796632 0.24910466223859992 chr19 59128983 1021126 0.017269466650559506 0.2287102505842764 chr20 63025520 828029 0.013137995529429984 0.1214816301341597 chr21 48129895 498845 0.010364556166183201 0.11290065245732973 chr22 51304566 860036 0.016763342272498708 0.13651061940514725 chrMT 16571 8685 0.5241083821133306 0.7866012915217372 chrX 155270560 2943720 0.018958648696829585 0.15943315449568546 chrY 59373566 129761 0.002185501204357508 0.059507407585166455