BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818851.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,183,382 number of mapped reads = 1,889,076 (86.52%) number of supplementary alignments = 30,809 (1.41%) number of secondary alignments = 0 number of mapped bases = 175,022,026 bp number of sequenced bases = 174,912,679 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 494,032 duplication rate = 22.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3707 >>>>>>> ACTG content number of A's = 51,816,310 bp (29.62%) number of C's = 35,503,317 bp (20.3%) number of T's = 50,022,414 bp (28.6%) number of G's = 37,567,895 bp (21.48%) number of N's = 2,743 bp (0%) GC percentage = 41.78% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,058,027 number of insertions = 23,329 mapped reads with insertion percentage = 1.19% number of deletions = 57,486 mapped reads with deletion percentage = 2.98% homopolymer indels = 41.97% >>>>>>> Coverage mean coverageData = 0.0565X std coverageData = 0.6479X There is a 3.69% of reference with a coverageData >= 1X There is a 1.15% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.15% 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 16596711 0.0665864379130273 1.0289906938718805 chr2 243199373 13250433 0.054483828788489515 0.923259777514562 chr3 198022430 10852856 0.054806195439577224 0.3309506994785934 chr4 191154276 8952233 0.04683250193158117 0.3901153655648872 chr5 180915260 7868122 0.04349064860531942 0.30751283562899134 chr6 171115067 8618505 0.050366721943895215 0.33770156830391623 chr7 159138663 15774223 0.0991225055095505 1.3392726570792355 chr8 146364022 15599228 0.10657829558687586 0.5810135592056889 chr9 141213431 6427650 0.045517270945707705 0.5404992305083701 chr10 135534747 8123802 0.05993888784844229 0.8295643347557867 chr11 135006516 7651496 0.056675012634205005 0.4109492490424357 chr12 133851895 6811851 0.05089095675485207 0.3205110047329289 chr13 115169878 5427512 0.04712614178509419 0.3051012397341783 chr14 107349540 5129091 0.04777934772706059 0.3380947934201799 chr15 102531392 4756924 0.046394805602561213 0.2986232979675532 chr16 90354753 4232262 0.04684050212610287 0.6569443465120257 chr17 81195210 4253764 0.052389346612934436 0.4085847180001668 chr18 78077248 3374772 0.04322350091027798 0.6193373887275867 chr19 59128983 2900062 0.04904637037305377 0.8003514563424841 chr20 63025520 7087101 0.11244811625512967 0.5066532037149672 chr21 48129895 1698152 0.03528268657141263 0.31857039165087725 chr22 51304566 1500310 0.029243206150501303 0.27285276820445314 chrMT 16571 248852 15.017319413433105 9.9066650291612 chrX 155270560 7271204 0.04682925082514032 0.35846955166758115 chrY 59373566 614910 0.010356629076313186 0.7242646864686373