BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714112.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 = 22,324 number of mapped reads = 5,905 (26.45%) number of supplementary alignments = 260 (1.16%) number of secondary alignments = 0 number of mapped bases = 670,848 bp number of sequenced bases = 658,722 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,256 duplication rate = 47.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 25.7815 >>>>>>> ACTG content number of A's = 140,282 bp (21.3%) number of C's = 123,625 bp (18.77%) number of T's = 129,574 bp (19.67%) number of G's = 265,239 bp (40.27%) number of N's = 2 bp (0%) GC percentage = 59.03% >>>>>>> Mismatches and indels general error rate = 0.0381 number of mismatches = 23,067 number of insertions = 385 mapped reads with insertion percentage = 5.06% number of deletions = 1,570 mapped reads with deletion percentage = 25.76% homopolymer indels = 34.27% >>>>>>> Coverage mean coverageData = 0.0002X std coverageData = 0.1888X 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 12591 5.05154207820409E-5 0.04477323373910883 chr2 243199373 171438 7.049278042341006E-4 0.6132222932379912 chr3 198022430 8373 4.228308883998646E-5 0.014172661950831663 chr4 191154276 4677 2.4467148200231734E-5 0.00906700128246305 chr5 180915260 8191 4.527534051024773E-5 0.019108526815683844 chr6 171115067 7817 4.568271010290403E-5 0.017859580231386736 chr7 159138663 15262 9.590378423626696E-5 0.05255984871012717 chr8 146364022 30070 2.0544666366164766E-4 0.12509222995687205 chr9 141213431 4089 2.8956169190450446E-5 0.00908559332454739 chr10 135534747 7975 5.884099964417243E-5 0.06363907760741593 chr11 135006516 7799 5.776758212173996E-5 0.020535030648568993 chr12 133851895 12974 9.692802630848072E-5 0.03402262289948003 chr13 115169878 1714 1.4882363598579136E-5 0.006267446364860498 chr14 107349540 7219 6.724761000373173E-5 0.0239804316793117 chr15 102531392 7764 7.572315023285747E-5 0.02224145184299267 chr16 90354753 6523 7.219321378699358E-5 0.018691531265137788 chr17 81195210 10646 1.3111610894287975E-4 0.039283296457178846 chr18 78077248 2877 3.684812251579359E-5 0.011669802156226938 chr19 59128983 6729 1.1380205879745979E-4 0.04467998316814275 chr20 63025520 10925 1.7334248095057366E-4 0.06830929029429303 chr21 48129895 768 1.5956818522043318E-5 0.005492549990503573 chr22 51304566 790 1.5398239603079382E-5 0.0055949101517629414 chrMT 16571 539 0.032526703276808885 0.21281909101959115 chrX 155270560 319806 0.0020596692637677096 0.3002012722617356 chrY 59373566 3292 5.544554962388481E-5 0.012687699087315698