BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-119_S31_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 = 20,827,644 number of mapped reads = 20,827,644 (100%) number of mapped paired reads (first in pair) = 10,413,822 number of mapped paired reads (second in pair) = 10,413,822 number of mapped paired reads (both in pair) = 20,827,644 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,931,242,379 bp number of sequenced bases = 1,927,081,899 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,652,981 duplication rate = 26.6% >>>>>>> Insert size mean insert size = 169.1509 std insert size = 92.8893 median insert size = 146 >>>>>>> Mapping quality mean mapping quality = 24.9509 >>>>>>> ACTG content number of A's = 750,369,034 bp (38.94%) number of C's = 214,529,918 bp (11.13%) number of T's = 748,927,130 bp (38.86%) number of G's = 213,255,817 bp (11.07%) number of N's = 25,192 bp (0%) GC percentage = 22.2% >>>>>>> Mismatches and indels general error rate = 0.1882 number of mismatches = 356,357,511 number of insertions = 2,186,842 mapped reads with insertion percentage = 9.16% number of deletions = 2,228,043 mapped reads with deletion percentage = 9.67% homopolymer indels = 52.03% >>>>>>> Coverage mean coverageData = 2.0494X std coverageData = 9.2873X There is a 47.88% of reference with a coverageData >= 1X There is a 33.97% of reference with a coverageData >= 2X There is a 24.21% of reference with a coverageData >= 3X There is a 18.13% of reference with a coverageData >= 4X There is a 13.6% of reference with a coverageData >= 5X There is a 10.45% of reference with a coverageData >= 6X There is a 8.04% of reference with a coverageData >= 7X There is a 6.3% of reference with a coverageData >= 8X There is a 4.96% of reference with a coverageData >= 9X There is a 3.97% of reference with a coverageData >= 10X There is a 3.2% of reference with a coverageData >= 11X There is a 2.62% of reference with a coverageData >= 12X There is a 2.17% of reference with a coverageData >= 13X There is a 1.82% of reference with a coverageData >= 14X There is a 1.54% of reference with a coverageData >= 15X There is a 1.32% of reference with a coverageData >= 16X There is a 1.14% of reference with a coverageData >= 17X There is a 0.99% of reference with a coverageData >= 18X There is a 0.88% of reference with a coverageData >= 19X There is a 0.78% of reference with a coverageData >= 20X There is a 0.7% of reference with a coverageData >= 21X There is a 0.63% of reference with a coverageData >= 22X There is a 0.57% of reference with a coverageData >= 23X There is a 0.52% of reference with a coverageData >= 24X There is a 0.48% of reference with a coverageData >= 25X There is a 0.44% of reference with a coverageData >= 26X There is a 0.41% of reference with a coverageData >= 27X There is a 0.38% of reference with a coverageData >= 28X There is a 0.36% of reference with a coverageData >= 29X There is a 0.33% of reference with a coverageData >= 30X There is a 0.31% of reference with a coverageData >= 31X There is a 0.3% of reference with a coverageData >= 32X There is a 0.28% of reference with a coverageData >= 33X There is a 0.26% of reference with a coverageData >= 34X There is a 0.25% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 193362387 2.1570065531651545 5.369833140799828 PGA_scaffold2__36_contigs__length_69596280 69596280 153724310 2.208800671530145 7.180180100682578 PGA_scaffold3__111_contigs__length_57743597 57743597 122874964 2.1279409386290915 5.7836311382802545 PGA_scaffold4__129_contigs__length_65288255 65288255 135345366 2.0730430917475124 7.670828398719305 PGA_scaffold5__109_contigs__length_67248332 67248332 120509932 1.79201369633971 5.83084345199436 PGA_scaffold6__104_contigs__length_61759565 61759565 120508063 1.951245333415156 11.078216410623108 PGA_scaffold7__69_contigs__length_43120122 43120122 86052049 1.995635564296409 5.231421512252937 PGA_scaffold8__63_contigs__length_61151155 61151155 125645395 2.054669204530969 6.327289093201772 PGA_scaffold9__45_contigs__length_38581958 38581958 86071489 2.2308740525817794 12.778439517133801 PGA_scaffold10__49_contigs__length_53961475 53961475 102079584 1.891712263239654 4.731536879176159 PGA_scaffold11__79_contigs__length_51449921 51449921 94448952 1.8357453260229495 6.3321271384627575 PGA_scaffold12__71_contigs__length_50438331 50438331 108375260 2.1486686385400025 6.906476717822632 PGA_scaffold13__52_contigs__length_44396874 44396874 88382594 1.9907391227589581 6.014368286072736 PGA_scaffold14__91_contigs__length_45393038 45393038 116723426 2.57139489099628 21.497089366230067 PGA_scaffold15__101_contigs__length_47938513 47938513 83393122 1.7395850805802007 5.5314408530161145 PGA_scaffold16__33_contigs__length_31980953 31980953 69956453 2.1874411622442897 22.60297830640715 PGA_scaffold17__51_contigs__length_34923512 34923512 72684226 2.0812404548545977 6.386889274853372 PGA_scaffold18__69_contigs__length_27737463 27737463 51104807 1.8424470543683105 8.52984139575137