BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549100.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 11,025,883 number of mapped reads = 9,393,207 (85.19%) number of secondary alignments = 0 number of mapped bases = 372,711,580 bp number of sequenced bases = 372,675,400 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 429,707 duplication rate = 3.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4304 >>>>>>> ACTG content number of A's = 113,274,384 bp (30.39%) number of C's = 72,900,379 bp (19.56%) number of T's = 113,814,085 bp (30.54%) number of G's = 72,684,947 bp (19.5%) number of N's = 1,605 bp (0%) GC percentage = 39.06% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 1,125,622 number of insertions = 9,419 mapped reads with insertion percentage = 0.1% number of deletions = 28,644 mapped reads with deletion percentage = 0.3% homopolymer indels = 45.15% >>>>>>> Coverage mean coverageData = 0.1204X std coverageData = 1.0703X There is a 9.56% of reference with a coverageData >= 1X There is a 1.76% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 29573258 0.11864868332665057 1.9673136043968453 chr2 243199373 32929358 0.13540066980353604 0.7185814692313546 chr3 198022430 27044003 0.13657040265590115 0.44429005589598514 chr4 191154276 27311713 0.14287785537164757 0.48049490754607993 chr5 180915260 24680546 0.13642047663640977 0.45537736322679667 chr6 171115067 23066979 0.13480390362118141 0.5314611249649732 chr7 159138663 21450040 0.13478836378058548 1.3361821458663192 chr8 146364022 20019266 0.136777233410544 2.945378408317936 chr9 141213431 15869123 0.11237686732503512 0.6792189955138827 chr10 135534747 17290621 0.12757334471580192 0.7228599690634501 chr11 135006516 17203179 0.12742480518495863 0.7083610988472276 chr12 133851895 17157336 0.12818149492765865 0.4683436770272166 chr13 115169878 13244615 0.11500068620373115 0.40123920596353907 chr14 107349540 11595191 0.10801342045806624 0.5451710157440411 chr15 102531392 10444614 0.10186747489003173 0.3782932929505953 chr16 90354753 9094528 0.10065356495413141 0.4691610531064293 chr17 81195210 7940889 0.09779996874199845 0.4375806066683397 chr18 78077248 10504678 0.13454211398434535 1.5473729989132634 chr19 59128983 5258968 0.08894061310000884 1.4826311290641996 chr20 63025520 6837233 0.1084835634834905 0.44409066401208896 chr21 48129895 4918337 0.10218881632714968 0.47391532524126695 chr22 51304566 3050391 0.05945652088743914 0.31523856186554894 chrMT 16571 121231 7.315852996198178 9.032668513434446 chrX 155270560 13045947 0.08402073773676091 0.4995408737182617 chrY 59373566 3059536 0.05153027190585117 0.447983003018809