BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237807.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,943,002 number of mapped reads = 2,111,906 (71.76%) number of supplementary alignments = 11,627 (0.4%) number of secondary alignments = 0 number of mapped bases = 134,580,140 bp number of sequenced bases = 134,529,405 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 153,013 duplication rate = 6.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6014 >>>>>>> ACTG content number of A's = 37,343,209 bp (27.76%) number of C's = 26,869,123 bp (19.97%) number of T's = 40,321,874 bp (29.97%) number of G's = 29,876,785 bp (22.21%) number of N's = 118,414 bp (0.09%) GC percentage = 42.18% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,095,790 number of insertions = 10,249 mapped reads with insertion percentage = 0.48% number of deletions = 29,662 mapped reads with deletion percentage = 1.39% homopolymer indels = 47.23% >>>>>>> Coverage mean coverageData = 0.0435X std coverageData = 0.393X There is a 2.78% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 10876442 0.04363656931470594 0.5558346526824747 chr2 243199373 11469858 0.04716236665626601 0.4260640075434183 chr3 198022430 9429240 0.047617030050585686 0.32883835200711525 chr4 191154276 8699227 0.04550893227206699 0.35087229933557207 chr5 180915260 8005268 0.04424871622216943 0.3122581792193618 chr6 171115067 7587099 0.04433916389139479 0.340064023975405 chr7 159138663 7235932 0.04546935272417112 0.44756582283559576 chr8 146364022 7119641 0.048643381773151875 0.4042832051932057 chr9 141213431 5153257 0.03649268319243656 0.35638150886361714 chr10 135534747 6430435 0.04744491831308764 0.5221042513666534 chr11 135006516 6052664 0.04483238423840224 0.40886053449582754 chr12 133851895 5985006 0.044713644136304534 0.315449798426978 chr13 115169878 4493229 0.03901392515150533 0.29427793267082225 chr14 107349540 3960678 0.036895155768715916 0.2972889651877403 chr15 102531392 3844398 0.03749483865390221 0.283790395606445 chr16 90354753 3980326 0.044052203872440444 0.34901470484551445 chr17 81195210 3741730 0.04608313717028381 0.35476477186913774 chr18 78077248 3636051 0.04656991752578165 0.6142394372492845 chr19 59128983 2466217 0.04170910566819659 0.44106288220272283 chr20 63025520 2904498 0.046084474987275 0.3348901663106017 chr21 48129895 1835550 0.038137419580907043 0.32142214706094074 chr22 51304566 1595863 0.031105671959100092 0.2623179746912308 chrMT 16571 66851 4.034216402148331 3.5780103168498947 chrX 155270560 7575559 0.04878940991775904 0.3515159765934155 chrY 59373566 435121 0.007328530679797808 0.21395155629591642