BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230390.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 = 3,960,678 number of mapped reads = 3,271,124 (82.59%) number of supplementary alignments = 20,162 (0.51%) number of secondary alignments = 0 number of mapped bases = 214,640,550 bp number of sequenced bases = 214,546,055 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 160,234 duplication rate = 3.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8872 >>>>>>> ACTG content number of A's = 58,421,704 bp (27.23%) number of C's = 37,164,222 bp (17.32%) number of T's = 71,283,767 bp (33.23%) number of G's = 47,260,249 bp (22.03%) number of N's = 416,113 bp (0.19%) GC percentage = 39.35% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 2,004,025 number of insertions = 19,318 mapped reads with insertion percentage = 0.59% number of deletions = 57,167 mapped reads with deletion percentage = 1.73% homopolymer indels = 48.14% >>>>>>> Coverage mean coverageData = 0.0693X std coverageData = 0.5375X There is a 5.71% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.16% 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 12452790 0.04996091865303718 0.6061655422523706 chr2 243199373 22297428 0.091683739661615 0.5827446537563301 chr3 198022430 15914274 0.08036601712240377 0.3274276747841586 chr4 191154276 21068786 0.11021875335919767 0.4107836157382939 chr5 180915260 13362238 0.07385909845305476 0.3174323327457731 chr6 171115067 20190908 0.11799608505544401 0.6257798506181593 chr7 159138663 13434362 0.08441922124229484 1.1589089893719862 chr8 146364022 11617430 0.07937353620960211 0.9518631261956371 chr9 141213431 7577691 0.05366126257494586 0.46114110233226546 chr10 135534747 10265384 0.0757398691274349 0.4680818930001861 chr11 135006516 8214289 0.060843648465085935 0.47066580582062595 chr12 133851895 7939443 0.05931513334196725 0.2932943572630064 chr13 115169878 6342072 0.05506710704338855 0.2694153288024116 chr14 107349540 6274634 0.05845049731931781 0.3110289363032787 chr15 102531392 4521370 0.04409742140241303 0.24134845270791475 chr16 90354753 2285545 0.025295238204015677 0.23656327609897268 chr17 81195210 4389125 0.054056452344910494 0.3537184467166913 chr18 78077248 7434232 0.09521636828183289 0.808613929267174 chr19 59128983 3745888 0.06335113188062105 0.40397548637912173 chr20 63025520 6038403 0.09580885647591643 0.3753149074068126 chr21 48129895 2217626 0.04607585368719379 0.2899114120520837 chr22 51304566 1987714 0.03874341320809536 0.22536921793302936 chrMT 16571 155028 9.355379880514151 6.000474000499844 chrX 155270560 4488260 0.02890605920401137 0.27271419953256276 chrY 59373566 425630 0.007168678398060174 0.18689626563010858