BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536764.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 21,223,508 number of mapped reads = 20,717,106 (97.61%) number of supplementary alignments = 519 (0%) number of secondary alignments = 0 number of mapped bases = 1,033,556,883 bp number of sequenced bases = 1,033,460,537 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 211,412 duplication rate = 1.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4131 >>>>>>> ACTG content number of A's = 314,518,533 bp (30.43%) number of C's = 200,195,520 bp (19.37%) number of T's = 313,959,545 bp (30.38%) number of G's = 204,750,368 bp (19.81%) number of N's = 36,571 bp (0%) GC percentage = 39.18% >>>>>>> Mismatches and indels general error rate = 0.0021 number of mismatches = 2,111,282 number of insertions = 64,816 mapped reads with insertion percentage = 0.31% number of deletions = 57,200 mapped reads with deletion percentage = 0.28% homopolymer indels = 48.85% >>>>>>> Coverage mean coverageData = 0.3339X std coverageData = 0.6745X There is a 24.86% of reference with a coverageData >= 1X There is a 6.34% of reference with a coverageData >= 2X There is a 1.6% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.03% 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 85556493 0.3432548840068888 0.6918449064353984 chr2 243199373 74646467 0.30693527733724874 0.6344089681168996 chr3 198022430 81360628 0.41086571859561566 0.7374112058054978 chr4 191154276 68392940 0.35778922361119453 0.6824410948691952 chr5 180915260 67723622 0.3743389142518989 0.6992498389659697 chr6 171115067 64799743 0.3786910418589849 0.7082767173289822 chr7 159138663 61493500 0.3864145823570228 0.725449589863639 chr8 146364022 56369381 0.3851314020326662 0.7136901120568081 chr9 141213431 48542042 0.3437494695529351 0.6976142932833334 chr10 135534747 49892677 0.36811724007571284 0.6945387236191835 chr11 135006516 50528713 0.3742686982604603 0.7226149495401641 chr12 133851895 51231405 0.3827469532650247 0.7178348468021951 chr13 115169878 40667121 0.3531055316390975 0.6931171165255526 chr14 107349540 35074516 0.32673187048589125 0.6723794615067347 chr15 102531392 29739239 0.2900500853436185 0.6320679821021111 chr16 90354753 22083545 0.2444093339505892 0.5697079589924872 chr17 81195210 15069200 0.18559222890118765 0.49735068683573586 chr18 78077248 42688529 0.5467473571814416 0.862311743548678 chr19 59128983 8844630 0.1495819740380111 0.43360595330782176 chr20 63025520 17886708 0.2838010380556955 0.6139726426013853 chr21 48129895 13796819 0.28665799083916554 0.6486048642962872 chr22 51304566 6717185 0.13092762542811492 0.4139811793031878 chrMT 16571 1496 0.09027819684991853 0.29671870529808997 chrX 155270560 35757220 0.23028976001632248 0.5424919476719574 chrY 59373566 4693064 0.07904298690767537 0.33084810035837214