BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-135_S35_L005_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 = 21,119,008 number of mapped reads = 21,119,008 (100%) number of mapped paired reads (first in pair) = 10,559,504 number of mapped paired reads (second in pair) = 10,559,504 number of mapped paired reads (both in pair) = 21,119,008 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,885,212,196 bp number of sequenced bases = 1,881,224,151 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,777,053 duplication rate = 32.24% >>>>>>> Insert size mean insert size = 152.7407 std insert size = 90.79 median insert size = 130 >>>>>>> Mapping quality mean mapping quality = 24.9555 >>>>>>> ACTG content number of A's = 727,470,103 bp (38.67%) number of C's = 214,288,835 bp (11.39%) number of T's = 726,077,483 bp (38.6%) number of G's = 213,387,730 bp (11.34%) number of N's = 25,543 bp (0%) GC percentage = 22.73% >>>>>>> Mismatches and indels general error rate = 0.1859 number of mismatches = 343,348,927 number of insertions = 2,129,514 mapped reads with insertion percentage = 8.84% number of deletions = 2,132,145 mapped reads with deletion percentage = 9.15% homopolymer indels = 51.12% >>>>>>> Coverage mean coverageData = 2.0005X std coverageData = 7.9608X There is a 44.29% of reference with a coverageData >= 1X There is a 31.66% of reference with a coverageData >= 2X There is a 22.53% of reference with a coverageData >= 3X There is a 17.27% of reference with a coverageData >= 4X There is a 13.15% of reference with a coverageData >= 5X There is a 10.39% of reference with a coverageData >= 6X There is a 8.15% of reference with a coverageData >= 7X There is a 6.58% of reference with a coverageData >= 8X There is a 5.27% of reference with a coverageData >= 9X There is a 4.33% of reference with a coverageData >= 10X There is a 3.54% of reference with a coverageData >= 11X There is a 2.96% of reference with a coverageData >= 12X There is a 2.46% of reference with a coverageData >= 13X There is a 2.1% of reference with a coverageData >= 14X There is a 1.78% of reference with a coverageData >= 15X There is a 1.54% of reference with a coverageData >= 16X There is a 1.32% of reference with a coverageData >= 17X There is a 1.16% of reference with a coverageData >= 18X There is a 1.02% of reference with a coverageData >= 19X There is a 0.9% of reference with a coverageData >= 20X There is a 0.8% of reference with a coverageData >= 21X There is a 0.72% of reference with a coverageData >= 22X There is a 0.65% of reference with a coverageData >= 23X There is a 0.59% of reference with a coverageData >= 24X There is a 0.54% of reference with a coverageData >= 25X There is a 0.5% of reference with a coverageData >= 26X There is a 0.46% of reference with a coverageData >= 27X There is a 0.42% of reference with a coverageData >= 28X There is a 0.39% of reference with a coverageData >= 29X There is a 0.37% of reference with a coverageData >= 30X There is a 0.34% of reference with a coverageData >= 31X There is a 0.32% 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 0.18% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 191236000 2.1332861659444218 5.341722417518611 PGA_scaffold2__36_contigs__length_69596280 69596280 151279456 2.173671581297161 6.245033989045378 PGA_scaffold3__111_contigs__length_57743597 57743597 120987771 2.0952586483311735 5.956049578782591 PGA_scaffold4__129_contigs__length_65288255 65288255 130580464 2.0000605621945327 7.186366244964698 PGA_scaffold5__109_contigs__length_67248332 67248332 116281336 1.7291333857916358 5.459772583124199 PGA_scaffold6__104_contigs__length_61759565 61759565 115644570 1.8724965112691452 8.389594860682076 PGA_scaffold7__69_contigs__length_43120122 43120122 85045926 1.972302536620838 5.51075248190254 PGA_scaffold8__63_contigs__length_61151155 61151155 123847997 2.0252764972305104 5.970006524013514 PGA_scaffold9__45_contigs__length_38581958 38581958 84316494 2.1853865996121815 12.699008358363455 PGA_scaffold10__49_contigs__length_53961475 53961475 101794132 1.8864223411239223 5.057855045874887 PGA_scaffold11__79_contigs__length_51449921 51449921 91363630 1.775777848133139 6.03574300871503 PGA_scaffold12__71_contigs__length_50438331 50438331 107078106 2.1229510151713784 7.1149502080323055 PGA_scaffold13__52_contigs__length_44396874 44396874 87906298 1.9800109800523342 6.311219288567585 PGA_scaffold14__91_contigs__length_45393038 45393038 113510049 2.5006048064022504 20.28970318760665 PGA_scaffold15__101_contigs__length_47938513 47938513 79444917 1.6572253085947826 5.479177330803884 PGA_scaffold16__33_contigs__length_31980953 31980953 65774841 2.056687960486981 9.536970450178766 PGA_scaffold17__51_contigs__length_34923512 34923512 70788805 2.026966961398384 5.850434669972913 PGA_scaffold18__69_contigs__length_27737463 27737463 48331404 1.7424594311311024 6.370330280645176