BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-226_S34_L004_dedup.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-226_S34_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 = 8,388,516 number of mapped reads = 8,388,516 (100%) number of mapped paired reads (first in pair) = 4,194,258 number of mapped paired reads (second in pair) = 4,194,258 number of mapped paired reads (both in pair) = 8,388,516 number of mapped paired reads (singletons) = 0 number of mapped bases = 775,156,835 bp number of sequenced bases = 771,065,057 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,373,346 duplication rate = 22.94% >>>>>>> Insert size mean insert size = 167.2982 std insert size = 94.1057 median insert size = 137 >>>>>>> Mapping quality mean mapping quality = 19.6401 >>>>>>> ACTG content number of A's = 292,657,344 bp (37.95%) number of C's = 94,309,293 bp (12.23%) number of T's = 291,335,749 bp (37.78%) number of G's = 92,762,671 bp (12.03%) number of N's = 48,412 bp (0.01%) GC percentage = 24.26% >>>>>>> Mismatches and indels general error rate = 0.212 number of mismatches = 153,183,192 number of insertions = 3,224,390 mapped reads with insertion percentage = 22.19% number of deletions = 1,951,452 mapped reads with deletion percentage = 17.6% homopolymer indels = 39.35% >>>>>>> Coverage mean coverageData = 0.8226X std coverageData = 7.1407X There is a 26.6% of reference with a coverageData >= 1X There is a 15.44% of reference with a coverageData >= 2X There is a 8.56% of reference with a coverageData >= 3X There is a 5.73% of reference with a coverageData >= 4X There is a 3.78% of reference with a coverageData >= 5X There is a 2.75% of reference with a coverageData >= 6X There is a 2% of reference with a coverageData >= 7X There is a 1.56% of reference with a coverageData >= 8X There is a 1.22% of reference with a coverageData >= 9X There is a 1% of reference with a coverageData >= 10X There is a 0.82% of reference with a coverageData >= 11X There is a 0.7% of reference with a coverageData >= 12X There is a 0.6% of reference with a coverageData >= 13X There is a 0.52% of reference with a coverageData >= 14X There is a 0.46% of reference with a coverageData >= 15X There is a 0.41% of reference with a coverageData >= 16X There is a 0.37% of reference with a coverageData >= 17X There is a 0.33% of reference with a coverageData >= 18X There is a 0.31% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.17% of reference with a coverageData >= 27X There is a 0.16% of reference with a coverageData >= 28X There is a 0.15% of reference with a coverageData >= 29X There is a 0.14% of reference with a coverageData >= 30X There is a 0.13% of reference with a coverageData >= 31X There is a 0.13% of reference with a coverageData >= 32X There is a 0.12% of reference with a coverageData >= 33X There is a 0.12% of reference with a coverageData >= 34X There is a 0.11% of reference with a coverageData >= 35X There is a 0.11% of reference with a coverageData >= 36X There is a 0.1% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.08% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.07% 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 0.06% of reference with a coverageData >= 49X There is a 0.06% 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 74664821 0.832905047804893 3.693987091428373 PGA_scaffold2__36_contigs__length_69596280 69596280 60306670 0.8665214577560755 4.445605479859431 PGA_scaffold3__111_contigs__length_57743597 57743597 48393443 0.8380746180394685 3.749306608944192 PGA_scaffold4__129_contigs__length_65288255 65288255 52915919 0.8104967578012309 8.471457986922136 PGA_scaffold5__109_contigs__length_67248332 67248332 49286780 0.73290710020882 4.407369827445842 PGA_scaffold6__104_contigs__length_61759565 61759565 47737952 0.7729645116509484 5.868957039843313 PGA_scaffold7__69_contigs__length_43120122 43120122 34707417 0.8049007143347137 3.5123041889218456 PGA_scaffold8__63_contigs__length_61151155 61151155 49638539 0.8117351013239243 3.761935389355012 PGA_scaffold9__45_contigs__length_38581958 38581958 36881659 0.9559302044753665 11.411669220428285 PGA_scaffold10__49_contigs__length_53961475 53961475 41352382 0.7663315726636457 4.2360770737090405 PGA_scaffold11__79_contigs__length_51449921 51449921 37032811 0.7197836319321074 4.176009803410372 PGA_scaffold12__71_contigs__length_50438331 50438331 43883503 0.8700427260370689 5.428221926314298 PGA_scaffold13__52_contigs__length_44396874 44396874 36231303 0.8160777941257756 4.39511674609295 PGA_scaffold14__91_contigs__length_45393038 45393038 48540667 1.0693416686497168 19.834833423058292 PGA_scaffold15__101_contigs__length_47938513 47938513 32620375 0.6804628045096017 3.416168960257856 PGA_scaffold16__33_contigs__length_31980953 31980953 29275423 0.9154018330848365 12.959561848595222 PGA_scaffold17__51_contigs__length_34923512 34923512 30056320 0.860632802336718 5.012475630635971 PGA_scaffold18__69_contigs__length_27737463 27737463 21630851 0.7798424462972695 6.6223985231220786