BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124790.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 628,702 number of mapped reads = 627,878 (99.87%) number of supplementary alignments = 252,845 (40.22%) number of secondary alignments = 0 number of mapped bases = 93,400,525 bp number of sequenced bases = 93,350,718 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 877,812 duplication rate = 17.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.319 >>>>>>> ACTG content number of A's = 26,722,253 bp (28.63%) number of C's = 17,642,467 bp (18.9%) number of T's = 29,741,185 bp (31.86%) number of G's = 19,244,813 bp (20.62%) number of N's = 0 bp (0%) GC percentage = 39.51% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 719,588 number of insertions = 18,512 mapped reads with insertion percentage = 2.93% number of deletions = 47,370 mapped reads with deletion percentage = 7.34% homopolymer indels = 73.43% >>>>>>> Coverage mean coverageData = 0.0302X std coverageData = 49.1579X There is a 0.01% 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 61335 2.4607762160801195E-4 0.14854099162302814 chr2 243199373 24921 1.0247148128955086E-4 0.017113524083671835 chr3 198022430 29276 1.478418379170481E-4 0.07021119308267099 chr4 191154276 12736 6.662681194743455E-5 0.00820061899769212 chr5 180915260 18799 1.0391052695057344E-4 0.010205316360621311 chr6 171115067 11761 6.873152789052761E-5 0.012343206644035586 chr7 159138663 19235 1.2086943321875213E-4 0.022188076932357494 chr8 146364022 67891948 0.46385680765181486 208.10517319192905 chr9 141213431 11356 8.041727985491692E-5 0.009068898346256887 chr10 135534747 25212486 0.18602230467143602 91.79230948224986 chr11 135006516 13694 1.0143214124568625E-4 0.010697481200858725 chr12 133851895 14501 1.0833615766142123E-4 0.010404671883912576 chr13 115169878 6898 5.989413308226306E-5 0.0077349707998456965 chr14 107349540 10955 1.0204980850406998E-4 0.03259758342320463 chr15 102531392 8627 8.414008462891053E-5 0.009163363470758164 chr16 90354753 8433 9.333211281093314E-5 0.009736291885761795 chr17 81195210 7990 9.84048196931814E-5 0.009916328368750468 chr18 78077248 6139 7.862725899355469E-5 0.008978100699760858 chr19 59128983 4077 6.895095760398924E-5 0.008302366742183792 chr20 63025520 5842 9.26926108662015E-5 0.009623957832266052 chr21 48129895 2655 5.516322028128256E-5 0.007898773894176621 chr22 51304566 2068 4.0308303163504006E-5 0.00634721896053685 chrMT 16571 303 0.018284955645404624 0.13376276206869853 chrX 155270560 11687 7.526861499050432E-5 0.00898288279366224 chrY 59373566 2803 4.720956123807689E-5 0.006857264932596034