BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716943.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 = 4,760,982 number of mapped reads = 4,027,282 (84.59%) number of supplementary alignments = 19,797 (0.42%) number of secondary alignments = 0 number of mapped bases = 231,666,616 bp number of sequenced bases = 231,603,542 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 225,740 duplication rate = 4.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9055 >>>>>>> ACTG content number of A's = 59,570,556 bp (25.72%) number of C's = 42,930,414 bp (18.54%) number of T's = 71,298,423 bp (30.78%) number of G's = 57,800,745 bp (24.96%) number of N's = 3,404 bp (0%) GC percentage = 43.49% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 1,141,802 number of insertions = 15,424 mapped reads with insertion percentage = 0.38% number of deletions = 40,310 mapped reads with deletion percentage = 0.99% homopolymer indels = 41.41% >>>>>>> Coverage mean coverageData = 0.0748X std coverageData = 0.5605X There is a 6.05% of reference with a coverageData >= 1X There is a 1% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 25957842 0.10414353992722851 0.9945826596324129 chr2 243199373 22088971 0.09082659518205255 0.7715869302460168 chr3 198022430 15999779 0.0807978116418428 0.35777391851295154 chr4 191154276 10645049 0.05568825988491097 0.3121197805419274 chr5 180915260 10218636 0.05648299651450077 0.29305660510994835 chr6 171115067 20079209 0.11734331378311648 0.5922740543695665 chr7 159138663 13074514 0.0821579982734931 0.748602374881429 chr8 146364022 16216706 0.11079707826012052 0.49117835373499197 chr9 141213431 9715463 0.06879985091503088 0.5011060759151674 chr10 135534747 14028907 0.10350782593042358 0.6906185952624823 chr11 135006516 7731141 0.057264947122996644 0.4472299763478791 chr12 133851895 10314657 0.07706022391390126 0.3552945800188367 chr13 115169878 5244924 0.045540761969028044 0.2591720483061098 chr14 107349540 5053877 0.04707870196742343 0.3413380911535043 chr15 102531392 6860741 0.066913565359573 0.3301121435400588 chr16 90354753 4940200 0.05467559631312367 0.3644650453923343 chr17 81195210 5325232 0.06558554377776718 0.3290477105129495 chr18 78077248 4422800 0.056646463768804965 0.9309832716896572 chr19 59128983 4406682 0.0745265989100472 0.7047592212744155 chr20 63025520 3992195 0.0633425158570687 0.3070114782698137 chr21 48129895 2139823 0.04445933239621653 0.3138788912496047 chr22 51304566 2848426 0.05551993169574809 0.28399155827176503 chrMT 16571 109705 6.620300525013578 4.308003971116455 chrX 155270560 9729083 0.06265890327181148 0.39580341254558743 chrY 59373566 522054 0.008792700778659648 0.18064104886880422