BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524613.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 = 2,006,211 number of mapped reads = 1,868,577 (93.14%) number of supplementary alignments = 4,283 (0.21%) number of secondary alignments = 0 number of mapped bases = 109,027,429 bp number of sequenced bases = 108,992,704 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,317 duplication rate = 3.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4582 >>>>>>> ACTG content number of A's = 27,036,367 bp (24.81%) number of C's = 19,211,996 bp (17.63%) number of T's = 36,086,518 bp (33.11%) number of G's = 26,657,170 bp (24.46%) number of N's = 653 bp (0%) GC percentage = 42.08% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 515,189 number of insertions = 7,234 mapped reads with insertion percentage = 0.39% number of deletions = 20,293 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.77% >>>>>>> Coverage mean coverageData = 0.0352X std coverageData = 0.3059X There is a 3.05% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% 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 11238629 0.04508967301630113 0.5404732789444551 chr2 243199373 9737059 0.040037352398930734 0.3557214651820689 chr3 198022430 7009191 0.03539594479271868 0.21363719362536968 chr4 191154276 4849207 0.025368027864571548 0.21187299685045283 chr5 180915260 6819019 0.037691784540452807 0.2194475032274423 chr6 171115067 7149187 0.0417799970823142 0.2514596019004516 chr7 159138663 6579181 0.04134244234539032 0.3954782314504758 chr8 146364022 9678692 0.06612753508509078 0.41258062723027206 chr9 141213431 3964379 0.028073668148463866 0.2678040924758071 chr10 135534747 4673587 0.034482574420565376 0.3104469427515372 chr11 135006516 5553786 0.04113717000148348 0.29549395468229755 chr12 133851895 3396033 0.025371572064781002 0.1855547211100245 chr13 115169878 2657098 0.02307111934250725 0.17358099596951834 chr14 107349540 2055370 0.019146518932451877 0.16450274333998935 chr15 102531392 2749473 0.02681591409585076 0.19380782915139416 chr16 90354753 3200046 0.03541646558427314 0.22582470568263976 chr17 81195210 2455821 0.030245885194459133 0.20506880300471017 chr18 78077248 2937681 0.037625314355342034 0.4646360456925232 chr19 59128983 2133947 0.03608969564046113 0.369974279038 chr20 63025520 2042380 0.032405603317513285 0.2080576959601046 chr21 48129895 939969 0.019529836913211633 0.17255828242458723 chr22 51304566 1964648 0.03829382359457051 0.220009695780944 chrMT 16571 15683 0.946412407217428 1.297591271543257 chrX 155270560 4963550 0.031967103100549135 0.23161341468394675 chrY 59373566 263813 0.0044432736278632815 0.12423977472739023