BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714200.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 123,164 number of mapped reads = 19,225 (15.61%) number of supplementary alignments = 750 (0.61%) number of secondary alignments = 0 number of mapped bases = 2,004,382 bp number of sequenced bases = 1,988,160 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,284 duplication rate = 46.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 26.493 >>>>>>> ACTG content number of A's = 186,986 bp (9.4%) number of C's = 134,608 bp (6.77%) number of T's = 159,474 bp (8.02%) number of G's = 1,507,022 bp (75.8%) number of N's = 70 bp (0%) GC percentage = 82.57% >>>>>>> Mismatches and indels general error rate = 0.0373 number of mismatches = 56,104 number of insertions = 2,525 mapped reads with insertion percentage = 8.64% number of deletions = 2,402 mapped reads with deletion percentage = 12.02% homopolymer indels = 52.89% >>>>>>> Coverage mean coverageData = 0.0006X std coverageData = 1.7008X There is a 0% 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 27863 1.117870835715992E-4 0.14699788818914072 chr2 243199373 1421538 0.0058451548721714834 6.059894442000826 chr3 198022430 8927 4.508075171080367E-5 0.011314540789046947 chr4 191154276 8539 4.467072449899054E-5 0.011817124594473101 chr5 180915260 17642 9.751526764519478E-5 0.036716363643116603 chr6 171115067 12097 7.06951188582359E-5 0.021201820296822656 chr7 159138663 16320 1.0255207435040472E-4 0.041659119757310285 chr8 146364022 26954 1.8415727876075992E-4 0.08118198044722874 chr9 141213431 7550 5.346516932939615E-5 0.01992341428310476 chr10 135534747 19737 1.456231736648315E-4 0.19657571233846552 chr11 135006516 7710 5.710835468119183E-5 0.014982483201038824 chr12 133851895 17679 1.3207881741233472E-4 0.038036216863454174 chr13 115169878 1826 1.5854840099769838E-5 0.004984977067131728 chr14 107349540 10688 9.95626064163852E-5 0.03980374984356967 chr15 102531392 9556 9.320072432060613E-5 0.033185156331121776 chr16 90354753 7671 8.489868817415725E-5 0.029165355165792294 chr17 81195210 15950 1.9644015946260868E-4 0.053551988119793746 chr18 78077248 4903 6.279678300136808E-5 0.015252460492148864 chr19 59128983 6515 1.1018285229089768E-4 0.03129951751075957 chr20 63025520 12278 1.948099753877477E-4 0.05603365038673223 chr21 48129895 2243 4.6603052011644734E-5 0.011705676711943055 chr22 51304566 1354 2.639141319312593E-5 0.006339612025628683 chrMT 16571 0 0.0 0.0 chrX 155270560 336760 0.0021688593124156957 0.2585887699586786 chrY 59373566 2082 3.5066110059820225E-5 0.00969693821495554