BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-205_S26_L004_dedup.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-205_S26_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 = 10,300,220 number of mapped reads = 10,300,220 (100%) number of mapped paired reads (first in pair) = 5,150,110 number of mapped paired reads (second in pair) = 5,150,110 number of mapped paired reads (both in pair) = 10,300,220 number of mapped paired reads (singletons) = 0 number of mapped bases = 899,546,254 bp number of sequenced bases = 894,823,167 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,224,299 duplication rate = 26.91% >>>>>>> Insert size mean insert size = 158.194 std insert size = 95.1053 median insert size = 126 >>>>>>> Mapping quality mean mapping quality = 19.7242 >>>>>>> ACTG content number of A's = 339,910,512 bp (37.99%) number of C's = 108,618,698 bp (12.14%) number of T's = 338,669,066 bp (37.85%) number of G's = 107,624,891 bp (12.03%) number of N's = 56,951 bp (0.01%) GC percentage = 24.17% >>>>>>> Mismatches and indels general error rate = 0.21 number of mismatches = 176,463,156 number of insertions = 3,630,676 mapped reads with insertion percentage = 21.13% number of deletions = 2,231,189 mapped reads with deletion percentage = 16.74% homopolymer indels = 40.12% >>>>>>> Coverage mean coverageData = 0.9546X std coverageData = 7.6143X There is a 28.79% of reference with a coverageData >= 1X There is a 17.78% of reference with a coverageData >= 2X There is a 10.15% of reference with a coverageData >= 3X There is a 7.04% of reference with a coverageData >= 4X There is a 4.72% of reference with a coverageData >= 5X There is a 3.5% of reference with a coverageData >= 6X There is a 2.56% of reference with a coverageData >= 7X There is a 2% of reference with a coverageData >= 8X There is a 1.56% of reference with a coverageData >= 9X There is a 1.27% of reference with a coverageData >= 10X There is a 1.04% of reference with a coverageData >= 11X There is a 0.88% of reference with a coverageData >= 12X There is a 0.75% of reference with a coverageData >= 13X There is a 0.65% of reference with a coverageData >= 14X There is a 0.57% of reference with a coverageData >= 15X There is a 0.51% of reference with a coverageData >= 16X There is a 0.45% of reference with a coverageData >= 17X There is a 0.41% of reference with a coverageData >= 18X There is a 0.37% of reference with a coverageData >= 19X There is a 0.34% of reference with a coverageData >= 20X There is a 0.31% of reference with a coverageData >= 21X There is a 0.29% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.15% of reference with a coverageData >= 32X There is a 0.14% of reference with a coverageData >= 33X There is a 0.14% of reference with a coverageData >= 34X There is a 0.13% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.12% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.11% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.1% 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 0.09% 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 0.08% of reference with a coverageData >= 47X There is a 0.08% 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 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 87381057 0.974757891106805 4.326982418744207 PGA_scaffold2__36_contigs__length_69596280 69596280 70175005 1.0083154588147527 5.307876042532124 PGA_scaffold3__111_contigs__length_57743597 57743597 55982301 0.9694979860710791 3.9344882975750455 PGA_scaffold4__129_contigs__length_65288255 65288255 61647153 0.9442303673149175 9.378148613503496 PGA_scaffold5__109_contigs__length_67248332 67248332 57142903 0.8497296706184475 4.7186044460632175 PGA_scaffold6__104_contigs__length_61759565 61759565 55874902 0.9047165730522875 7.055153084515836 PGA_scaffold7__69_contigs__length_43120122 43120122 40061368 0.929064347266921 3.59220477747365 PGA_scaffold8__63_contigs__length_61151155 61151155 57651141 0.942764547946805 3.8202849077367675 PGA_scaffold9__45_contigs__length_38581958 38581958 42269021 1.0955644345473603 12.41564540480729 PGA_scaffold10__49_contigs__length_53961475 53961475 47776295 0.8853778552198582 3.913782743523931 PGA_scaffold11__79_contigs__length_51449921 51449921 43274250 0.841094585937265 4.586368852087393 PGA_scaffold12__71_contigs__length_50438331 50438331 50203963 0.9953533751939572 5.221926459103512 PGA_scaffold13__52_contigs__length_44396874 44396874 41888345 0.943497621026201 4.746502786450632 PGA_scaffold14__91_contigs__length_45393038 45393038 55612621 1.2251354712147708 18.41089899512913 PGA_scaffold15__101_contigs__length_47938513 47938513 38273017 0.7983772254262455 3.72146877351325 PGA_scaffold16__33_contigs__length_31980953 31980953 34794457 1.0879743639909667 17.09719204631079 PGA_scaffold17__51_contigs__length_34923512 34923512 34192767 0.9790758443767053 5.0323908912725805 PGA_scaffold18__69_contigs__length_27737463 27737463 25345688 0.9137709530247954 8.092307938879468