BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714145.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 = 38,806 number of mapped reads = 7,453 (19.21%) number of supplementary alignments = 220 (0.57%) number of secondary alignments = 0 number of mapped bases = 837,385 bp number of sequenced bases = 823,674 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,802 duplication rate = 37.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.3455 >>>>>>> ACTG content number of A's = 189,711 bp (23.03%) number of C's = 137,215 bp (16.66%) number of T's = 179,817 bp (21.83%) number of G's = 316,911 bp (38.48%) number of N's = 20 bp (0%) GC percentage = 55.13% >>>>>>> Mismatches and indels general error rate = 0.0417 number of mismatches = 29,061 number of insertions = 1,157 mapped reads with insertion percentage = 14.21% number of deletions = 2,252 mapped reads with deletion percentage = 28.07% homopolymer indels = 37.61% >>>>>>> Coverage mean coverageData = 0.0003X std coverageData = 0.2305X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 59079 2.37026490698292E-4 0.05998613596498591 chr2 243199373 237895 9.78189199525609E-4 0.7673970699860451 chr3 198022430 30234 1.5267967371171033E-4 0.055204540451296816 chr4 191154276 34305 1.7946237310432963E-4 0.10573005614175081 chr5 180915260 40457 2.2362403259957176E-4 0.056862650806787846 chr6 171115067 13352 7.802936488345588E-5 0.02855191163486392 chr7 159138663 25064 1.5749786712736176E-4 0.05279149313309212 chr8 146364022 22385 1.5294059082361102E-4 0.04932849625103158 chr9 141213431 10647 7.539651097352064E-5 0.020200787614716997 chr10 135534747 17322 1.278048646816746E-4 0.030373061641163143 chr11 135006516 18013 1.33423189737005E-4 0.026718837540624575 chr12 133851895 30551 2.282448074418371E-4 0.05815992797049553 chr13 115169878 28454 2.470611282578592E-4 0.08486282134875997 chr14 107349540 10483 9.765295687340625E-5 0.03055067603476942 chr15 102531392 14264 1.391183687431065E-4 0.032446732558793004 chr16 90354753 4046 4.477904997427197E-5 0.010833686557651689 chr17 81195210 59924 7.380238317014021E-4 0.34000438671647065 chr18 78077248 4781 6.123422792770564E-5 0.013875749254127842 chr19 59128983 7821 1.3227015928888883E-4 0.0381168124504401 chr20 63025520 11915 1.890504037094815E-4 0.060432774912907355 chr21 48129895 1814 3.7689672915347106E-5 0.008638864734827943 chr22 51304566 4519 8.808182881812118E-5 0.02131886466250864 chrMT 16571 32230 1.94496409389898 13.988635182836031 chrX 155270560 113801 7.329206515388364E-4 0.08662375613966694 chrY 59373566 4029 6.785848099472415E-5 0.023710371544555114