BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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 = 20,533,044 number of mapped reads = 20,533,044 (100%) number of mapped paired reads (first in pair) = 10,266,522 number of mapped paired reads (second in pair) = 10,266,522 number of mapped paired reads (both in pair) = 20,533,044 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,866,305,145 bp number of sequenced bases = 1,862,106,260 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,057,472 duplication rate = 29.81% >>>>>>> Insert size mean insert size = 152.2396 std insert size = 87.1267 median insert size = 130 >>>>>>> Mapping quality mean mapping quality = 24.5085 >>>>>>> ACTG content number of A's = 721,855,131 bp (38.77%) number of C's = 210,617,088 bp (11.31%) number of T's = 720,101,097 bp (38.67%) number of G's = 209,532,944 bp (11.25%) number of N's = 166,894 bp (0.01%) GC percentage = 22.56% >>>>>>> Mismatches and indels general error rate = 0.1871 number of mismatches = 341,867,643 number of insertions = 2,215,908 mapped reads with insertion percentage = 9.41% number of deletions = 2,167,633 mapped reads with deletion percentage = 9.54% homopolymer indels = 50.43% >>>>>>> Coverage mean coverageData = 1.9805X std coverageData = 9.9461X There is a 44.89% of reference with a coverageData >= 1X There is a 32.01% of reference with a coverageData >= 2X There is a 22.52% of reference with a coverageData >= 3X There is a 17.07% of reference with a coverageData >= 4X There is a 12.84% of reference with a coverageData >= 5X There is a 10.02% of reference with a coverageData >= 6X There is a 7.77% of reference with a coverageData >= 7X There is a 6.19% of reference with a coverageData >= 8X There is a 4.91% of reference with a coverageData >= 9X There is a 3.99% of reference with a coverageData >= 10X There is a 3.23% of reference with a coverageData >= 11X There is a 2.68% of reference with a coverageData >= 12X There is a 2.22% of reference with a coverageData >= 13X There is a 1.87% of reference with a coverageData >= 14X There is a 1.59% of reference with a coverageData >= 15X There is a 1.37% of reference with a coverageData >= 16X There is a 1.18% of reference with a coverageData >= 17X There is a 1.04% of reference with a coverageData >= 18X There is a 0.91% of reference with a coverageData >= 19X There is a 0.81% of reference with a coverageData >= 20X There is a 0.73% of reference with a coverageData >= 21X There is a 0.66% of reference with a coverageData >= 22X There is a 0.6% of reference with a coverageData >= 23X There is a 0.55% of reference with a coverageData >= 24X There is a 0.5% of reference with a coverageData >= 25X There is a 0.47% of reference with a coverageData >= 26X There is a 0.43% of reference with a coverageData >= 27X There is a 0.4% of reference with a coverageData >= 28X There is a 0.38% of reference with a coverageData >= 29X There is a 0.35% of reference with a coverageData >= 30X There is a 0.33% of reference with a coverageData >= 31X There is a 0.31% of reference with a coverageData >= 32X There is a 0.3% of reference with a coverageData >= 33X There is a 0.28% of reference with a coverageData >= 34X There is a 0.27% of reference with a coverageData >= 35X There is a 0.25% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 189546243 2.114436497305108 5.645814638849571 PGA_scaffold2__36_contigs__length_69596280 69596280 150475428 2.162118837386136 7.560819898010911 PGA_scaffold3__111_contigs__length_57743597 57743597 118522432 2.0525640617781398 6.070866029539524 PGA_scaffold4__129_contigs__length_65288255 65288255 129643935 1.9857160372872578 9.26209929514669 PGA_scaffold5__109_contigs__length_67248332 67248332 116742679 1.7359936749063158 6.313840648212309 PGA_scaffold6__104_contigs__length_61759565 61759565 114927620 1.8608877831312445 8.334751397666352 PGA_scaffold7__69_contigs__length_43120122 43120122 83918716 1.9461613768161417 6.025152877949674 PGA_scaffold8__63_contigs__length_61151155 61151155 121756328 1.9910715995470567 6.62667564084318 PGA_scaffold9__45_contigs__length_38581958 38581958 84308533 2.18518025964364 16.62390093682637 PGA_scaffold10__49_contigs__length_53961475 53961475 99944181 1.8521395310265334 5.092643844067143 PGA_scaffold11__79_contigs__length_51449921 51449921 89908714 1.747499553983766 6.551600733158182 PGA_scaffold12__71_contigs__length_50438331 50438331 105897682 2.0995477031149186 8.087058557653629 PGA_scaffold13__52_contigs__length_44396874 44396874 86892569 1.9571776382274122 7.0605837638336295 PGA_scaffold14__91_contigs__length_45393038 45393038 112964109 2.4885778519604704 28.49036168833101 PGA_scaffold15__101_contigs__length_47938513 47938513 78067968 1.62850207723381 5.757423298714958 PGA_scaffold16__33_contigs__length_31980953 31980953 65919513 2.0612116530736277 13.807640551700667 PGA_scaffold17__51_contigs__length_34923512 34923512 68818395 1.9705462325782126 5.782920804406757 PGA_scaffold18__69_contigs__length_27737463 27737463 48050100 1.7323177682111734 8.315984107437908