BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716350.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 478,504 number of mapped reads = 432,488 (90.38%) number of supplementary alignments = 9,039 (1.89%) number of secondary alignments = 0 number of mapped bases = 33,717,877 bp number of sequenced bases = 33,702,767 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,571 duplication rate = 1.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0447 >>>>>>> ACTG content number of A's = 8,841,855 bp (26.23%) number of C's = 6,514,226 bp (19.33%) number of T's = 10,450,979 bp (31.01%) number of G's = 7,893,305 bp (23.42%) number of N's = 2,402 bp (0.01%) GC percentage = 42.75% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 235,267 number of insertions = 2,807 mapped reads with insertion percentage = 0.64% number of deletions = 7,844 mapped reads with deletion percentage = 1.79% homopolymer indels = 42.15% >>>>>>> Coverage mean coverageData = 0.0109X std coverageData = 0.137X There is a 1.03% of reference with a coverageData >= 1X There is a 0.04% 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 3319784 0.013319060095741948 0.24624145635867076 chr2 243199373 2867170 0.011789380723444546 0.14306072497055725 chr3 198022430 2196100 0.011090157816970533 0.1085175377629581 chr4 191154276 2209635 0.011559432758909353 0.12216449383155402 chr5 180915260 2035408 0.01125061534333809 0.10976653639248277 chr6 171115067 1859455 0.010866693579940568 0.11079882612422248 chr7 159138663 1757489 0.011043758737623678 0.15143230626515305 chr8 146364022 960341 0.006561318737196222 0.12078178169538237 chr9 141213431 1440050 0.010197684383151912 0.12084940230453668 chr10 135534747 1620803 0.011958579153137756 0.1424265827253719 chr11 135006516 1915338 0.014187004129489571 0.1450513601737014 chr12 133851895 1515350 0.011321094856370917 0.10995171559801659 chr13 115169878 1173128 0.010186066186507551 0.104451703437333 chr14 107349540 994212 0.009261446299630162 0.10146195178892924 chr15 102531392 955609 0.009320160210055472 0.09953020596699927 chr16 90354753 771048 0.0085335632537228 0.09730842002840794 chr17 81195210 1056077 0.01300664164794943 0.1252684770765462 chr18 78077248 862941 0.011052400310010927 0.1622118388049154 chr19 59128983 656818 0.01110822420199583 0.16570473275967923 chr20 63025520 708605 0.011243144047046339 0.11192624019077047 chr21 48129895 466435 0.009691170113709992 0.10638269098141691 chr22 51304566 385605 0.00751599769891826 0.08964338040377645 chrMT 16571 3608 0.21772976887333292 0.45188949849355603 chrX 155270560 1881819 0.012119612372107114 0.12007240286713218 chrY 59373566 105049 0.001769289046913571 0.07486045898067971