BamQC report ----------------------------------- >>>>>>> Input bam file = /Users/strigg/Desktop/20200427/Sealice_F2_S22.dedup.sorted.bam outfile = /Users/strigg/Desktop/20200427/Sealice_F2_S22.dedup.sorted_stats/genome_results.txt >>>>>>> Reference number of bases = 506,970,227 bp number of contigs = 21 >>>>>>> Globals number of windows = 420 number of reads = 53,248,360 number of mapped reads = 53,248,360 (100%) number of mapped paired reads (first in pair) = 26,624,180 number of mapped paired reads (second in pair) = 26,624,180 number of mapped paired reads (both in pair) = 53,248,360 number of mapped paired reads (singletons) = 0 number of mapped bases = 6,199,394,588 bp number of sequenced bases = 6,173,223,853 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,562,236 duplication rate = 24.88% >>>>>>> Insert size mean insert size = 142.2101 std insert size = 63.7368 median insert size = 133 >>>>>>> Mapping quality mean mapping quality = 16.1308 >>>>>>> ACTG content number of A's = 2,410,240,743 bp (39.04%) number of C's = 675,087,412 bp (10.94%) number of T's = 2,409,933,267 bp (39.04%) number of G's = 677,962,431 bp (10.98%) number of N's = 43,660 bp (0%) GC percentage = 21.92% >>>>>>> Mismatches and indels general error rate = 0.229 number of mismatches = 1,343,814,679 number of insertions = 38,168,816 mapped reads with insertion percentage = 45.32% number of deletions = 15,516,752 mapped reads with deletion percentage = 23.86% homopolymer indels = 56.14% >>>>>>> Coverage mean coverageData = 12.2283X std coverageData = 42.6626X There is a 73.84% of reference with a coverageData >= 1X There is a 67.68% of reference with a coverageData >= 2X There is a 58.45% of reference with a coverageData >= 3X There is a 53.84% of reference with a coverageData >= 4X There is a 48.35% of reference with a coverageData >= 5X There is a 44.85% of reference with a coverageData >= 6X There is a 41.03% of reference with a coverageData >= 7X There is a 38.28% of reference with a coverageData >= 8X There is a 35.42% of reference with a coverageData >= 9X There is a 33.19% of reference with a coverageData >= 10X There is a 30.95% of reference with a coverageData >= 11X There is a 29.12% of reference with a coverageData >= 12X There is a 27.3% of reference with a coverageData >= 13X There is a 25.77% of reference with a coverageData >= 14X There is a 24.25% of reference with a coverageData >= 15X There is a 22.95% of reference with a coverageData >= 16X There is a 21.68% of reference with a coverageData >= 17X There is a 20.56% of reference with a coverageData >= 18X There is a 19.47% of reference with a coverageData >= 19X There is a 18.5% of reference with a coverageData >= 20X There is a 17.56% of reference with a coverageData >= 21X There is a 16.71% of reference with a coverageData >= 22X There is a 15.88% of reference with a coverageData >= 23X There is a 15.13% of reference with a coverageData >= 24X There is a 14.41% of reference with a coverageData >= 25X There is a 13.74% of reference with a coverageData >= 26X There is a 13.1% of reference with a coverageData >= 27X There is a 12.51% of reference with a coverageData >= 28X There is a 11.93% of reference with a coverageData >= 29X There is a 11.4% of reference with a coverageData >= 30X There is a 10.89% of reference with a coverageData >= 31X There is a 10.42% of reference with a coverageData >= 32X There is a 9.95% of reference with a coverageData >= 33X There is a 9.52% of reference with a coverageData >= 34X There is a 9.1% of reference with a coverageData >= 35X There is a 8.71% of reference with a coverageData >= 36X There is a 8.33% of reference with a coverageData >= 37X There is a 7.97% of reference with a coverageData >= 38X There is a 7.63% of reference with a coverageData >= 39X There is a 7.3% of reference with a coverageData >= 40X There is a 6.99% of reference with a coverageData >= 41X There is a 6.69% of reference with a coverageData >= 42X There is a 6.41% of reference with a coverageData >= 43X There is a 6.14% of reference with a coverageData >= 44X There is a 5.88% of reference with a coverageData >= 45X There is a 5.63% of reference with a coverageData >= 46X There is a 5.4% of reference with a coverageData >= 47X There is a 5.17% of reference with a coverageData >= 48X There is a 4.96% of reference with a coverageData >= 49X There is a 4.75% of reference with a coverageData >= 50X There is a 4.55% of reference with a coverageData >= 51X >>>>>>> Coverage per contig Cr_scaffold0000001 36897007 464506567 12.589274978320057 37.94078312503891 Cr_scaffold0000002 35124817 413185688 11.763354895201305 34.48611545171961 Cr_scaffold0000003 33138466 405102476 12.224539180540221 34.56806483371149 Cr_scaffold0000004 31456035 405661622 12.89614606545294 34.143941779806795 Cr_scaffold0000005 30612693 363314193 11.868089912899855 27.714287736505817 Cr_scaffold0000006 30259679 368168819 12.166977019154764 27.390681911223243 Cr_scaffold0000007 29872177 349932184 11.714318109456837 27.639072612360724 Cr_scaffold0000008 27803016 337074794 12.123677301771865 72.78367516296647 Cr_scaffold0000009 25126635 301755889 12.009403129388396 31.201564001940845 Cr_scaffold0000010 24815513 299448975 12.067007238576934 28.081387184016478 Cr_scaffold0000011 35794548 474026835 13.242989826271867 24.893525880194197 Cr_scaffold0000012 22957860 253685098 11.050032450759783 20.89795949002403 Cr_scaffold0000013 21502856 244210870 11.357136465965265 22.21854440747952 Cr_scaffold0000014 21148584 256212990 12.114900458583893 40.106389710018554 Cr_scaffold0000015 19091682 239034545 12.520350223725703 59.3003514472854 Cr_scaffold0000016 18525937 222909213 12.032277395739822 66.26555314258442 Cr_scaffold0000017 17562062 225440852 12.836809937238577 96.91776905929815 Cr_scaffold0000018 14680182 171115564 11.656229057650648 37.457898826503055 Cr_scaffold0000019 14290452 199010886 13.926143553751833 66.96338741124787 Cr_scaffold0000020 8286978 97530248 11.769097009790542 32.969144358460625 Cr_scaffold0000021 8023048 108066280 13.469479429762853 29.664590948951084