BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-227_S35_L004_dedup.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-227_S35_L004_dedup.sorted_stats/genome_results.txt >>>>>>> Reference number of bases = 942,353,201 bp number of contigs = 18 >>>>>>> Globals number of windows = 417 number of reads = 9,840,976 number of mapped reads = 9,840,976 (100%) number of mapped paired reads (first in pair) = 4,920,488 number of mapped paired reads (second in pair) = 4,920,488 number of mapped paired reads (both in pair) = 9,840,976 number of mapped paired reads (singletons) = 0 number of mapped bases = 889,082,160 bp number of sequenced bases = 884,278,852 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,849,523 duplication rate = 24.46% >>>>>>> Insert size mean insert size = 165.6601 std insert size = 96.7926 median insert size = 133 >>>>>>> Mapping quality mean mapping quality = 19.6713 >>>>>>> ACTG content number of A's = 336,326,256 bp (38.03%) number of C's = 107,213,002 bp (12.12%) number of T's = 335,010,833 bp (37.89%) number of G's = 105,728,761 bp (11.96%) number of N's = 56,749 bp (0.01%) GC percentage = 24.08% >>>>>>> Mismatches and indels general error rate = 0.2138 number of mismatches = 177,460,807 number of insertions = 3,726,566 mapped reads with insertion percentage = 22.01% number of deletions = 2,293,855 mapped reads with deletion percentage = 17.64% homopolymer indels = 39.62% >>>>>>> Coverage mean coverageData = 0.9435X std coverageData = 7.6315X There is a 29.53% of reference with a coverageData >= 1X There is a 17.74% of reference with a coverageData >= 2X There is a 10.14% of reference with a coverageData >= 3X There is a 6.86% of reference with a coverageData >= 4X There is a 4.56% of reference with a coverageData >= 5X There is a 3.32% of reference with a coverageData >= 6X There is a 2.42% of reference with a coverageData >= 7X There is a 1.87% of reference with a coverageData >= 8X There is a 1.46% of reference with a coverageData >= 9X There is a 1.18% of reference with a coverageData >= 10X There is a 0.97% of reference with a coverageData >= 11X There is a 0.82% of reference with a coverageData >= 12X There is a 0.7% of reference with a coverageData >= 13X There is a 0.61% of reference with a coverageData >= 14X There is a 0.53% of reference with a coverageData >= 15X There is a 0.48% of reference with a coverageData >= 16X There is a 0.43% of reference with a coverageData >= 17X There is a 0.38% of reference with a coverageData >= 18X There is a 0.35% of reference with a coverageData >= 19X There is a 0.32% of reference with a coverageData >= 20X There is a 0.29% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.16% of reference with a coverageData >= 30X There is a 0.15% of reference with a coverageData >= 31X There is a 0.14% of reference with a coverageData >= 32X There is a 0.14% of reference with a coverageData >= 33X There is a 0.13% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 86033098 0.959721065995632 3.5454687775570775 PGA_scaffold2__36_contigs__length_69596280 69596280 68817947 0.9888164568566021 4.831860372679992 PGA_scaffold3__111_contigs__length_57743597 57743597 55537882 0.9618015656350608 3.896905194345401 PGA_scaffold4__129_contigs__length_65288255 65288255 60838646 0.9318467157684027 9.147352053056013 PGA_scaffold5__109_contigs__length_67248332 67248332 56414939 0.8389046586315331 4.768202399504886 PGA_scaffold6__104_contigs__length_61759565 61759565 55268557 0.894898741595735 5.413347094312807 PGA_scaffold7__69_contigs__length_43120122 43120122 39251520 0.9102831388093011 3.510939573512627 PGA_scaffold8__63_contigs__length_61151155 61151155 56950326 0.9313041756938197 3.7560304313449953 PGA_scaffold9__45_contigs__length_38581958 38581958 42058465 1.0901070650691185 12.692409008097101 PGA_scaffold10__49_contigs__length_53961475 53961475 47407646 0.8785461479694542 4.35200287523849 PGA_scaffold11__79_contigs__length_51449921 51449921 42771854 0.831329828475344 4.230928085745203 PGA_scaffold12__71_contigs__length_50438331 50438331 49853959 0.988414128929048 5.495426611560183 PGA_scaffold13__52_contigs__length_44396874 44396874 41310330 0.930478348543188 4.508206161576523 PGA_scaffold14__91_contigs__length_45393038 45393038 56147495 1.2369186437796915 21.4745176011415 PGA_scaffold15__101_contigs__length_47938513 47938513 37634218 0.7850518433894685 3.5301020575656756 PGA_scaffold16__33_contigs__length_31980953 31980953 33872063 1.0591323842038103 14.23678916674141 PGA_scaffold17__51_contigs__length_34923512 34923512 34013608 0.9739458047632781 5.143221261206185 PGA_scaffold18__69_contigs__length_27737463 27737463 24899607 0.8976886963310236 7.425035112384932