BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236069.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 = 1,890,937 number of mapped reads = 1,662,145 (87.9%) number of supplementary alignments = 9,057 (0.48%) number of secondary alignments = 0 number of mapped bases = 109,960,020 bp number of sequenced bases = 109,908,835 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,592 duplication rate = 3.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7394 >>>>>>> ACTG content number of A's = 30,158,819 bp (27.44%) number of C's = 19,728,341 bp (17.95%) number of T's = 35,332,054 bp (32.15%) number of G's = 24,632,064 bp (22.41%) number of N's = 57,557 bp (0.05%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 863,069 number of insertions = 7,853 mapped reads with insertion percentage = 0.47% number of deletions = 29,516 mapped reads with deletion percentage = 1.76% homopolymer indels = 47.76% >>>>>>> Coverage mean coverageData = 0.0355X std coverageData = 0.3746X There is a 3% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 12224578 0.049045326149859424 0.826810953114893 chr2 243199373 7325846 0.03012279969981666 0.3886375264587041 chr3 198022430 11304280 0.057085856385056984 0.2728249829617823 chr4 191154276 6419904 0.03358493534301058 0.22131833487778968 chr5 180915260 4123376 0.02279175344302078 0.17640978877997973 chr6 171115067 8917651 0.052114937371353746 0.3508924314106843 chr7 159138663 5059687 0.03179420327290295 0.4412991511625696 chr8 146364022 5030707 0.03437119950147312 0.50537102838702 chr9 141213431 3851885 0.027277044206935247 0.29854625217618896 chr10 135534747 5020955 0.037045518666884734 0.31705147894588287 chr11 135006516 4231199 0.031340702103593285 0.2565551998572947 chr12 133851895 3384871 0.025288181388840255 0.192265201565147 chr13 115169878 3078678 0.026731625086899892 0.18687312187164823 chr14 107349540 3046865 0.028382655389114848 0.2048982402109627 chr15 102531392 3259296 0.03178827417070471 0.20898709193423906 chr16 90354753 1895498 0.020978398336167218 0.17760970484009866 chr17 81195210 3071182 0.03782466970650116 0.22986537112364783 chr18 78077248 4367683 0.05594053468687831 0.4749333136175818 chr19 59128983 2792045 0.04721956743277658 0.4596622338773104 chr20 63025520 2778143 0.044079652178990354 0.24396211665578885 chr21 48129895 1519002 0.03156046777164172 0.21535478883135964 chr22 51304566 1422298 0.02772263973541848 0.18734540112431927 chrMT 16571 44911 2.7102166435338844 2.2844253017645766 chrX 155270560 5554569 0.03577348468376748 0.23627564029530748 chrY 59373566 234911 0.003956491344986757 0.10858607623509033