BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083653.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,518,721 number of mapped reads = 2,087,553 (82.88%) number of supplementary alignments = 14,616 (0.58%) number of secondary alignments = 0 number of mapped bases = 122,813,211 bp number of sequenced bases = 122,777,415 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,705 duplication rate = 2.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8219 >>>>>>> ACTG content number of A's = 36,770,917 bp (29.95%) number of C's = 24,332,807 bp (19.82%) number of T's = 35,662,887 bp (29.05%) number of G's = 25,994,938 bp (21.17%) number of N's = 15,866 bp (0.01%) GC percentage = 40.99% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 988,102 number of insertions = 8,339 mapped reads with insertion percentage = 0.4% number of deletions = 23,085 mapped reads with deletion percentage = 1.1% homopolymer indels = 46.18% >>>>>>> Coverage mean coverageData = 0.0397X std coverageData = 0.3203X There is a 3.45% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.06% 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% 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 9835833 0.03946161883384034 0.6596786988801506 chr2 243199373 11670642 0.0479879608900143 0.28109471515888307 chr3 198022430 10954289 0.055318425291518744 0.2659581023085453 chr4 191154276 5764547 0.030156516090699432 0.1958231534301328 chr5 180915260 5491950 0.030356477391680504 0.1948181302516772 chr6 171115067 8819293 0.051540131179681564 0.2905914051644918 chr7 159138663 8096304 0.05087578246148769 0.414906845540584 chr8 146364022 8440633 0.05766876917334234 0.40676777907121014 chr9 141213431 5022472 0.03556653191154317 0.23808784803213245 chr10 135534747 5012830 0.03698557093997453 0.2746793511326575 chr11 135006516 5052353 0.03742303075208607 0.25606396202407755 chr12 133851895 4559936 0.03406702609626856 0.20553432827226722 chr13 115169878 3903059 0.03388958178804357 0.2048248186744207 chr14 107349540 2604959 0.02426614031136044 0.1747756440147363 chr15 102531392 3457298 0.03371940956385338 0.20589415537893033 chr16 90354753 3429224 0.03795288998244509 0.2247353996601968 chr17 81195210 2524961 0.0310974132587378 0.20712283947831706 chr18 78077248 3288082 0.04211319025998457 0.3781401354762125 chr19 59128983 3321441 0.056172807842813734 0.46288016178163854 chr20 63025520 2379725 0.03775811766408274 0.2201848907515313 chr21 48129895 1917024 0.03983021363333537 0.22589790400070203 chr22 51304566 844505 0.01646062067847918 0.1414513685190163 chrMT 16571 200338 12.089674732967232 7.193286751608078 chrX 155270560 5966894 0.03842901062506634 0.22677215485759733 chrY 59373566 254619 0.004288423572200464 0.08596635774817343