BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234087.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 = 913,801 number of mapped reads = 523,483 (57.29%) number of supplementary alignments = 2,128 (0.23%) number of secondary alignments = 0 number of mapped bases = 31,487,608 bp number of sequenced bases = 31,465,907 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,037 duplication rate = 4.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9257 >>>>>>> ACTG content number of A's = 8,358,265 bp (26.56%) number of C's = 5,059,715 bp (16.08%) number of T's = 10,500,157 bp (33.37%) number of G's = 7,543,067 bp (23.97%) number of N's = 4,703 bp (0.01%) GC percentage = 40.05% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 298,254 number of insertions = 2,537 mapped reads with insertion percentage = 0.48% number of deletions = 12,519 mapped reads with deletion percentage = 2.36% homopolymer indels = 47.46% >>>>>>> Coverage mean coverageData = 0.0102X std coverageData = 0.1337X There is a 0.89% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% 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 2585338 0.010372443565546823 0.15205864691919582 chr2 243199373 2142833 0.008811013669841985 0.13009455969048903 chr3 198022430 2598509 0.013122296297444689 0.12859626011908382 chr4 191154276 1598756 0.00836369467351073 0.1048528994493374 chr5 180915260 1814973 0.010032171968246349 0.11282267149375816 chr6 171115067 1988484 0.011620741731644239 0.12976594836475994 chr7 159138663 2205653 0.013859944267597624 0.19931112579929652 chr8 146364022 1491002 0.01018694334595424 0.19036464024037741 chr9 141213431 1222110 0.008654346766774613 0.11724215567599024 chr10 135534747 1482043 0.010934782650238024 0.1270170758150746 chr11 135006516 1431505 0.010603228958223024 0.13807831508974508 chr12 133851895 1489367 0.011126977320717052 0.11823246841096949 chr13 115169878 1424858 0.01237179395119269 0.127102177366458 chr14 107349540 1347856 0.012555768753177703 0.12900252007130478 chr15 102531392 697745 0.006805184113759033 0.09284136018127692 chr16 90354753 804070 0.008899033789622555 0.10866213826351193 chr17 81195210 787626 0.009700399814225494 0.11447352686172306 chr18 78077248 712019 0.009119417221262716 0.1801491460895734 chr19 59128983 695074 0.011755216557673587 0.13263255148350012 chr20 63025520 698335 0.011080194181658478 0.12414903631028719 chr21 48129895 487563 0.010130148839925789 0.11321147139863554 chr22 51304566 295743 0.005764457689789248 0.08371753612890498 chrMT 16571 79822 4.8169694043811475 3.828004274304063 chrX 155270560 1288117 0.008295951273699276 0.10436448099639381 chrY 59373566 118207 0.001990902820288746 0.05243108083018995