BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716766.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 = 1,160,540 number of mapped reads = 1,049,677 (90.45%) number of supplementary alignments = 3,707 (0.32%) number of secondary alignments = 0 number of mapped bases = 60,066,209 bp number of sequenced bases = 60,047,176 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,048 duplication rate = 2.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4397 >>>>>>> ACTG content number of A's = 14,623,894 bp (24.35%) number of C's = 11,449,017 bp (19.07%) number of T's = 20,158,308 bp (33.57%) number of G's = 13,814,831 bp (23.01%) number of N's = 1,126 bp (0%) GC percentage = 42.07% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 317,746 number of insertions = 4,206 mapped reads with insertion percentage = 0.4% number of deletions = 11,882 mapped reads with deletion percentage = 1.12% homopolymer indels = 42.72% >>>>>>> Coverage mean coverageData = 0.0194X std coverageData = 0.2106X There is a 1.78% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% 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 4869622 0.01953705062183175 0.32815057625509053 chr2 243199373 5046609 0.020750912873447252 0.32802807513679594 chr3 198022430 4039974 0.020401597940192938 0.15524001134870855 chr4 191154276 3887859 0.020338854465384807 0.16992217395188175 chr5 180915260 3598563 0.019890875982490366 0.15039008703651885 chr6 171115067 3450101 0.020162461789527863 0.17302629615469212 chr7 159138663 3304228 0.02076320070629222 0.23468876394737345 chr8 146364022 3037474 0.020752873271000984 0.2276289202034523 chr9 141213431 2532312 0.01793251521521349 0.17509761768110965 chr10 135534747 2952869 0.02178680423552198 0.23317951412806498 chr11 135006516 2682942 0.019872685256169413 0.17890891292591032 chr12 133851895 2704394 0.02020437588873882 0.15426352051751224 chr13 115169878 1883931 0.016357844887184825 0.13618841874778892 chr14 107349540 1796410 0.016734212368306377 0.14223201035658348 chr15 102531392 1729447 0.016867487764137643 0.14123383312033722 chr16 90354753 1782060 0.01972292481392761 0.16039775226176234 chr17 81195210 1659397 0.020437129234594013 0.15951645699455094 chr18 78077248 1545895 0.019799557996716278 0.26457919926265555 chr19 59128983 1260636 0.021320102867319737 0.253675464938083 chr20 63025520 1263589 0.02004884687980361 0.15452553550403111 chr21 48129895 785417 0.01631869340251002 0.15339103575080976 chr22 51304566 711480 0.013867771535188506 0.12608487270704483 chrMT 16571 18471 1.114658137710458 1.1697249778147456 chrX 155270560 3308426 0.02130749061509149 0.1683602810359319 chrY 59373566 214103 0.003606032354532992 0.14467541239872622