BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716804.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 = 486,532 number of mapped reads = 372,459 (76.55%) number of supplementary alignments = 1,595 (0.33%) number of secondary alignments = 0 number of mapped bases = 21,455,522 bp number of sequenced bases = 21,449,398 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,150 duplication rate = 1.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6911 >>>>>>> ACTG content number of A's = 5,466,863 bp (25.49%) number of C's = 4,097,948 bp (19.11%) number of T's = 6,816,598 bp (31.78%) number of G's = 5,067,682 bp (23.63%) number of N's = 307 bp (0%) GC percentage = 42.73% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 107,676 number of insertions = 1,575 mapped reads with insertion percentage = 0.42% number of deletions = 3,909 mapped reads with deletion percentage = 1.04% homopolymer indels = 41.72% >>>>>>> Coverage mean coverageData = 0.0069X std coverageData = 0.0972X There is a 0.66% of reference with a coverageData >= 1X There is a 0.02% 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 1722722 0.0069116056485171206 0.1387624629226542 chr2 243199373 1807452 0.0074319763974062545 0.11533645197122494 chr3 198022430 1428264 0.007212637477481717 0.08743173863685307 chr4 191154276 1352262 0.007074191738195802 0.08831329384859089 chr5 180915260 1274339 0.00704384472597834 0.08628753509130156 chr6 171115067 1232693 0.007203883454634652 0.09165164144667401 chr7 159138663 1183660 0.007437915951323532 0.1088382872093206 chr8 146364022 1066249 0.007284911861741542 0.09378588583054229 chr9 141213431 899305 0.00636840981506922 0.08828781448211082 chr10 135534747 1039335 0.007668402553627079 0.09762743851289556 chr11 135006516 975873 0.007228340001011507 0.09256679345092945 chr12 133851895 980653 0.007326403559695587 0.08830227697249826 chr13 115169878 660911 0.005738575150700429 0.07814194953311927 chr14 107349540 639345 0.005955731156370116 0.08040733561287011 chr15 102531392 621248 0.006059100416777722 0.08083829338277868 chr16 90354753 636532 0.007044809253144657 0.08774593561977141 chr17 81195210 609157 0.007502376063809675 0.09001765463107139 chr18 78077248 560582 0.007179838100851096 0.10794822268400177 chr19 59128983 468476 0.00792295040826256 0.11458075853296304 chr20 63025520 467116 0.007411537421666652 0.0886659901941569 chr21 48129895 280601 0.005830077127739423 0.07971496130557973 chr22 51304566 269807 0.005258927636187391 0.07481953751551242 chrMT 16571 3018 0.18212539979482228 0.45178793412612916 chrX 155270560 1207647 0.007777694625433179 0.0931394754561348 chrY 59373566 68275 0.0011499225092863716 0.043661529546106866