BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716325.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 = 3,594,440 number of mapped reads = 3,289,861 (91.53%) number of supplementary alignments = 16,721 (0.47%) number of secondary alignments = 0 number of mapped bases = 191,917,541 bp number of sequenced bases = 191,862,378 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 180,764 duplication rate = 4.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9367 >>>>>>> ACTG content number of A's = 46,763,206 bp (24.37%) number of C's = 37,578,799 bp (19.59%) number of T's = 59,844,353 bp (31.19%) number of G's = 47,670,420 bp (24.85%) number of N's = 5,600 bp (0%) GC percentage = 44.43% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 933,933 number of insertions = 10,797 mapped reads with insertion percentage = 0.33% number of deletions = 35,010 mapped reads with deletion percentage = 1.06% homopolymer indels = 43.7% >>>>>>> Coverage mean coverageData = 0.062X std coverageData = 0.5344X There is a 5.17% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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% 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 20183641 0.08097729473660971 1.0591999740162958 chr2 243199373 15595117 0.06412482403891724 0.6558268489200677 chr3 198022430 18102796 0.09141790654725326 0.3614155722444183 chr4 191154276 9239211 0.04833379191580313 0.27698545772110383 chr5 180915260 8877354 0.049069127723111915 0.2631008281769046 chr6 171115067 14454028 0.08446963936846076 0.6280527882994845 chr7 159138663 11546709 0.07255753430578966 0.7022651674707977 chr8 146364022 13703327 0.09362496884651066 0.44154755583058614 chr9 141213431 7353354 0.0520726247349659 0.44455653365530234 chr10 135534747 8393436 0.06192829651277543 0.5643024278714577 chr11 135006516 6601743 0.04889943978703961 0.41124857676729915 chr12 133851895 8153328 0.06091305618048964 0.30456835424127077 chr13 115169878 4546024 0.03947233494508 0.2350106196796995 chr14 107349540 4437864 0.04134031687513519 0.27816045213467894 chr15 102531392 5794519 0.05651458433335227 0.2840351872195893 chr16 90354753 4273520 0.04729712447999277 0.3182636033979065 chr17 81195210 4281097 0.05272597977146681 0.2867914867294251 chr18 78077248 3882580 0.049727418671313826 0.8683660979955447 chr19 59128983 3682579 0.06228043868097647 0.7279049962128741 chr20 63025520 2695080 0.042761725726340696 0.24656760140735046 chr21 48129895 1883401 0.039131624949524615 0.27563216488813413 chr22 51304566 3090066 0.06022984387003683 0.28850479508459237 chrMT 16571 10207 0.6159555850582342 0.94082797758431 chrX 155270560 10681549 0.06879313760444994 0.3834549521842183 chrY 59373566 455011 0.007663528244202142 0.1526224281684266