BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716199.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 = 2,208,137 number of mapped reads = 1,800,697 (81.55%) number of supplementary alignments = 39,743 (1.8%) number of secondary alignments = 0 number of mapped bases = 134,750,582 bp number of sequenced bases = 134,702,158 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,094 duplication rate = 2.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0089 >>>>>>> ACTG content number of A's = 34,712,371 bp (25.77%) number of C's = 27,285,336 bp (20.26%) number of T's = 40,699,326 bp (30.21%) number of G's = 31,988,382 bp (23.75%) number of N's = 16,743 bp (0.01%) GC percentage = 44% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 996,751 number of insertions = 11,075 mapped reads with insertion percentage = 0.61% number of deletions = 28,157 mapped reads with deletion percentage = 1.54% homopolymer indels = 40.6% >>>>>>> Coverage mean coverageData = 0.0435X std coverageData = 0.3572X There is a 3.74% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 10739998 0.04308915242381683 0.39124814462711194 chr2 243199373 11536809 0.04743765930679435 0.5312032880450676 chr3 198022430 9040623 0.04565454024576913 0.23961821216334547 chr4 191154276 8750650 0.04577794534923195 0.26092954166754456 chr5 180915260 8143035 0.04501021638528447 0.24205377220015964 chr6 171115067 7866593 0.04597253262332533 0.28372327977258266 chr7 159138663 7401776 0.046511487909132426 0.4673714747536202 chr8 146364022 6897858 0.04712809818795496 0.47221699717583476 chr9 141213431 5708686 0.040425942203755394 0.38938331880939 chr10 135534747 6345909 0.046821270120495376 0.3284399096749882 chr11 135006516 6043161 0.04476199504326147 0.3880101203510292 chr12 133851895 6092843 0.04551928831489461 0.2439878815374032 chr13 115169878 4266502 0.03704529408288511 0.21621867666323513 chr14 107349540 4094555 0.03814226870464466 0.26839012810495166 chr15 102531392 3839921 0.03745117397801446 0.2207389072617379 chr16 90354753 3944226 0.043652667613401586 0.2677704552421384 chr17 81195210 3644802 0.044889372168629156 0.26607060541823113 chr18 78077248 3713560 0.04756263950286772 0.7409475261311961 chr19 59128983 2648500 0.04479190856369033 0.36267327713450886 chr20 63025520 2849864 0.04521761978322432 0.25252226422842405 chr21 48129895 1802242 0.037445375685943215 0.23916375174594742 chr22 51304566 1508683 0.029406407998851407 0.19484483784192494 chrMT 16571 7929 0.47848651258222197 0.8794668363759489 chrX 155270560 7526284 0.0484720606404717 0.3256048255674011 chrY 59373566 335573 0.005651892291596567 0.1541627213061664