BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013181.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 = 2,767,734 number of mapped reads = 2,505,237 (90.52%) number of supplementary alignments = 11,838 (0.43%) number of secondary alignments = 0 number of mapped bases = 165,829,712 bp number of sequenced bases = 165,764,214 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,469 duplication rate = 2.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6423 >>>>>>> ACTG content number of A's = 45,408,829 bp (27.39%) number of C's = 31,399,930 bp (18.94%) number of T's = 51,001,185 bp (30.77%) number of G's = 37,914,357 bp (22.87%) number of N's = 39,913 bp (0.02%) GC percentage = 41.81% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,258,141 number of insertions = 11,861 mapped reads with insertion percentage = 0.47% number of deletions = 37,552 mapped reads with deletion percentage = 1.48% homopolymer indels = 46.92% >>>>>>> Coverage mean coverageData = 0.0536X std coverageData = 0.4077X There is a 4.51% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12203442 0.04896052796594637 0.44826810616327506 chr2 243199373 16592862 0.06822740451719832 0.5395712830590963 chr3 198022430 10511308 0.05308140093018755 0.26394247591801806 chr4 191154276 10300307 0.053884784664717626 0.27817656850646116 chr5 180915260 9028505 0.04990460727304043 0.25760537396734307 chr6 171115067 8853590 0.051740563558906244 0.3140058162053008 chr7 159138663 10118683 0.06358406442059904 0.6959418188265534 chr8 146364022 9016680 0.06160448364831078 0.449783018865544 chr9 141213431 6042865 0.04279242390194457 0.33390946779813346 chr10 135534747 7728809 0.05702455769515695 0.3754640056338942 chr11 135006516 6946735 0.05145481274400118 0.3167945617242136 chr12 133851895 8252598 0.061654696782589447 0.2910279705396942 chr13 115169878 4218852 0.036631557428583886 0.24460532594858886 chr14 107349540 5529272 0.0515071792575916 0.2751445328485379 chr15 102531392 4717093 0.046006329456640946 0.25864360135561193 chr16 90354753 5363806 0.059363849957068664 0.3115583973259653 chr17 81195210 4391493 0.05408561662689215 0.28658384046158386 chr18 78077248 3952029 0.0506169095509104 0.5373806221257834 chr19 59128983 3476515 0.05879544723439603 0.40569581410126027 chr20 63025520 3833213 0.06082001386105184 0.28868677503127615 chr21 48129895 2738050 0.056888759055053 0.29147694494532295 chr22 51304566 1746957 0.034050711977565505 0.21062945268243163 chrMT 16571 713401 43.05117373725182 50.88446713615587 chrX 155270560 9176906 0.059102678576028835 0.29659686938817903 chrY 59373566 375741 0.006328422315075365 0.12783370464965643