BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081882.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 = 3,073,590 number of mapped reads = 2,804,255 (91.24%) number of supplementary alignments = 19,164 (0.62%) number of secondary alignments = 0 number of mapped bases = 188,595,864 bp number of sequenced bases = 188,527,194 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,233 duplication rate = 3.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8966 >>>>>>> ACTG content number of A's = 51,775,483 bp (27.46%) number of C's = 36,273,878 bp (19.24%) number of T's = 57,754,181 bp (30.63%) number of G's = 42,721,493 bp (22.66%) number of N's = 2,159 bp (0%) GC percentage = 41.9% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,556,710 number of insertions = 13,602 mapped reads with insertion percentage = 0.48% number of deletions = 38,617 mapped reads with deletion percentage = 1.36% homopolymer indels = 46.12% >>>>>>> Coverage mean coverageData = 0.0609X std coverageData = 0.4712X There is a 5.04% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% 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 15376228 0.061689828247208256 0.7751813430344637 chr2 243199373 15632201 0.06427730798467149 0.5999513401801012 chr3 198022430 13124861 0.06627966841938057 0.30279187392833495 chr4 191154276 13185818 0.0689799792917005 0.3414144680404078 chr5 180915260 11129759 0.06151918306946578 0.2899185699575515 chr6 171115067 10744304 0.06278993538307179 0.360254705759679 chr7 159138663 10266106 0.06451044520840293 0.6748787093242475 chr8 146364022 9753151 0.0666362598316682 0.5755856135340128 chr9 141213431 7503318 0.053134591708914714 0.4323882277012268 chr10 135534747 8911608 0.0657514637187466 0.547661137217027 chr11 135006516 8962551 0.06638606243271991 0.40329581206288523 chr12 133851895 8483051 0.06337639821983843 0.29764320530609834 chr13 115169878 6054956 0.05257412880128257 0.26680484543762156 chr14 107349540 5769855 0.05374829738441357 0.29613235586698744 chr15 102531392 5476494 0.05341285135385658 0.27479526871606796 chr16 90354753 4995416 0.05528669864218432 0.33111168506535116 chr17 81195210 4818712 0.05934724474510258 0.3191538319851445 chr18 78077248 5244723 0.06717351257052502 0.8092322218379562 chr19 59128983 3497452 0.059149537545741315 0.6012452817430337 chr20 63025520 3842636 0.06096952472585708 0.30008414243137604 chr21 48129895 2661638 0.05530113872053949 0.31111237168898415 chr22 51304566 2064722 0.040244410214872496 0.23286092615853857 chrMT 16571 28995 1.749743527849858 1.731086939950328 chrX 155270560 10566473 0.06805200547998282 0.34422899605156 chrY 59373566 500836 0.008435336358270951 0.20584294317263946