BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714070.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 352,028 number of mapped reads = 287,513 (81.67%) number of supplementary alignments = 7,539 (2.14%) number of secondary alignments = 0 number of mapped bases = 37,239,022 bp number of sequenced bases = 36,318,869 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 254,685 duplication rate = 43.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.8714 >>>>>>> ACTG content number of A's = 9,838,331 bp (27.09%) number of C's = 7,952,438 bp (21.9%) number of T's = 9,235,862 bp (25.43%) number of G's = 9,291,967 bp (25.58%) number of N's = 271 bp (0%) GC percentage = 47.48% >>>>>>> Mismatches and indels general error rate = 0.0469 number of mismatches = 1,606,423 number of insertions = 40,021 mapped reads with insertion percentage = 13.5% number of deletions = 136,585 mapped reads with deletion percentage = 45.25% homopolymer indels = 29.1% >>>>>>> Coverage mean coverageData = 0.012X std coverageData = 3.9191X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 3069474 0.012314809839530951 4.134460059728003 chr2 243199373 3808783 0.01566115468562495 6.01538886948157 chr3 198022430 1422630 0.007184186155073443 1.6530955440039665 chr4 191154276 1470633 0.0076934350137163555 2.371406418424955 chr5 180915260 2200301 0.012162053107073445 3.378931283158781 chr6 171115067 2038091 0.011910646068355863 2.539091501571278 chr7 159138663 1036204 0.006511327797192817 1.019497098919525 chr8 146364022 1310210 0.008951721755774108 1.6325773027718908 chr9 141213431 1234392 0.008741321496536685 2.077755505617175 chr10 135534747 2146899 0.01584021107148265 3.1610632497536217 chr11 135006516 1470039 0.010888652218830681 2.2186682717084523 chr12 133851895 2401863 0.01794418375623296 4.180035530362329 chr13 115169878 1170581 0.010163951028931367 2.4182651291520165 chr14 107349540 2542873 0.023687786645382923 13.42967377386966 chr15 102531392 1035506 0.010099404482872913 1.6786292148513546 chr16 90354753 711036 0.0078693812598879 1.248732845799254 chr17 81195210 729729 0.008987340509372412 1.4647924438848599 chr18 78077248 1190278 0.015244876458760432 3.087049434275524 chr19 59128983 778050 0.013158521600143198 1.7319031339568915 chr20 63025520 923515 0.014653032612820966 2.3829939981192063 chr21 48129895 500333 0.01039547250206966 2.3914195354381413 chr22 51304566 175517 0.0034210795195109924 0.49876896260730647 chrMT 16571 222894 13.450847866755174 115.47735690220745 chrX 155270560 3390076 0.02183334690104808 3.2771690596646255 chrY 59373566 259115 0.004364147506316194 1.1668825372287561