BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240199.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,609,573 number of mapped reads = 1,216,168 (75.56%) number of supplementary alignments = 5,490 (0.34%) number of secondary alignments = 0 number of mapped bases = 73,400,044 bp number of sequenced bases = 73,356,884 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 134,884 duplication rate = 9.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4988 >>>>>>> ACTG content number of A's = 20,020,114 bp (27.29%) number of C's = 12,763,463 bp (17.4%) number of T's = 23,981,551 bp (32.69%) number of G's = 16,575,366 bp (22.6%) number of N's = 16,390 bp (0.02%) GC percentage = 39.99% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 718,843 number of insertions = 5,113 mapped reads with insertion percentage = 0.42% number of deletions = 25,468 mapped reads with deletion percentage = 2.07% homopolymer indels = 50.64% >>>>>>> Coverage mean coverageData = 0.0237X std coverageData = 0.2536X There is a 1.64% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 5625993 0.02257163082454266 0.30774252457594825 chr2 243199373 7563650 0.03110061472074601 0.30347531665743277 chr3 198022430 4998231 0.025240731567631 0.21810775286849654 chr4 191154276 4987840 0.02609326929207694 0.22836270485617594 chr5 180915260 3956026 0.021866734735367266 0.20380449534887465 chr6 171115067 4264993 0.024924707536128306 0.23998912044128862 chr7 159138663 4371445 0.027469408863891234 0.3733570990636005 chr8 146364022 4415036 0.030164762758432533 0.3484867544177342 chr9 141213431 2710245 0.019192544085980038 0.2264157549019932 chr10 135534747 3535766 0.026087524256787082 0.24671394361077326 chr11 135006516 3368811 0.024952951159779576 0.2532814759776758 chr12 133851895 3218302 0.024043753732436886 0.21189011591078213 chr13 115169878 1809522 0.015711764494532154 0.1713214327956078 chr14 107349540 2423189 0.022572886665373694 0.21220290537559183 chr15 102531392 1853321 0.018075644579174346 0.19185862070917764 chr16 90354753 1912019 0.021161244278981094 0.2011821693112886 chr17 81195210 1991089 0.024522247063589096 0.22185477863326208 chr18 78077248 1665680 0.021333743730311806 0.3124149993881167 chr19 59128983 1162109 0.019653796514646632 0.24110595109180744 chr20 63025520 1536158 0.02437358708028113 0.21876280164862677 chr21 48129895 1121968 0.02331124969210924 0.20960657848356573 chr22 51304566 724514 0.01412182299719678 0.15860452566786679 chrMT 16571 47572 2.8707983827167944 3.787676940928013 chrX 155270560 3966441 0.025545351288743984 0.23013456465940504 chrY 59373566 170124 0.002865315517683408 0.0769191718116911