BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238034.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,011,511 number of mapped reads = 1,826,894 (90.82%) number of supplementary alignments = 12,681 (0.63%) number of secondary alignments = 0 number of mapped bases = 122,172,337 bp number of sequenced bases = 122,118,976 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,239 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9026 >>>>>>> ACTG content number of A's = 33,013,899 bp (27.03%) number of C's = 23,220,480 bp (19.01%) number of T's = 37,965,651 bp (31.09%) number of G's = 27,911,826 bp (22.86%) number of N's = 7,120 bp (0.01%) GC percentage = 41.87% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 885,109 number of insertions = 8,409 mapped reads with insertion percentage = 0.46% number of deletions = 29,832 mapped reads with deletion percentage = 1.62% homopolymer indels = 46.36% >>>>>>> Coverage mean coverageData = 0.0395X std coverageData = 0.3801X There is a 3.36% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 14333842 0.057507748395940805 0.8123156837605087 chr2 243199373 8706818 0.035801153155111134 0.3935008388555694 chr3 198022430 5314319 0.026836954783354593 0.1889620218501949 chr4 191154276 9376939 0.04905429894751609 0.26698153878274644 chr5 180915260 6600940 0.03648636383685931 0.21750145250153366 chr6 171115067 7646492 0.04468625781504092 0.30290676562108704 chr7 159138663 6335097 0.039808660451043254 0.48496527934807454 chr8 146364022 6143363 0.041973176987442996 0.3649118441274932 chr9 141213431 4384657 0.03104985813991022 0.3274317303499885 chr10 135534747 7886668 0.05818927009174998 0.43658464327484275 chr11 135006516 5193478 0.03846835066834848 0.2657721001040962 chr12 133851895 6540946 0.04886704069449297 0.2568429847578528 chr13 115169878 2464216 0.021396358516590597 0.16425747908003377 chr14 107349540 2699138 0.025143451942132217 0.2152365125496323 chr15 102531392 4522480 0.04410824735511247 0.23954103168961755 chr16 90354753 5026759 0.05563358686841853 0.2985115486426946 chr17 81195210 2599232 0.03201213470597588 0.2166634723621951 chr18 78077248 2634056 0.033736537435335834 0.5636192723035732 chr19 59128983 2313304 0.0391230134974586 0.5048943885222761 chr20 63025520 3526186 0.05594854274903246 0.2734517083126135 chr21 48129895 898781 0.018674069411537257 0.19361785712207177 chr22 51304566 1386275 0.027020499500960596 0.18709802854352364 chrMT 16571 15296 0.9230583549574558 1.0757327267179242 chrX 155270560 5339040 0.034385397978857035 0.23283501920226618 chrY 59373566 284015 0.0047835260560229785 0.13398941992476873