BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-175_S14_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 = 15,849,240 number of mapped reads = 15,849,240 (100%) number of mapped paired reads (first in pair) = 7,924,620 number of mapped paired reads (second in pair) = 7,924,620 number of mapped paired reads (both in pair) = 15,849,240 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,434,658,947 bp number of sequenced bases = 1,431,434,458 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,301,239 duplication rate = 29.21% >>>>>>> Insert size mean insert size = 152.0107 std insert size = 88.5963 median insert size = 128 >>>>>>> Mapping quality mean mapping quality = 24.2795 >>>>>>> ACTG content number of A's = 551,983,579 bp (38.56%) number of C's = 165,400,387 bp (11.55%) number of T's = 550,260,947 bp (38.44%) number of G's = 163,789,545 bp (11.44%) number of N's = 129,337 bp (0.01%) GC percentage = 23% >>>>>>> Mismatches and indels general error rate = 0.1856 number of mismatches = 260,444,291 number of insertions = 1,724,773 mapped reads with insertion percentage = 9.48% number of deletions = 1,659,913 mapped reads with deletion percentage = 9.46% homopolymer indels = 49.99% >>>>>>> Coverage mean coverageData = 1.5224X std coverageData = 8.4272X There is a 39.19% of reference with a coverageData >= 1X There is a 26.43% of reference with a coverageData >= 2X There is a 17.49% of reference with a coverageData >= 3X There is a 12.78% of reference with a coverageData >= 4X There is a 9.24% of reference with a coverageData >= 5X There is a 7.03% of reference with a coverageData >= 6X There is a 5.31% of reference with a coverageData >= 7X There is a 4.15% of reference with a coverageData >= 8X There is a 3.25% of reference with a coverageData >= 9X There is a 2.61% of reference with a coverageData >= 10X There is a 2.1% of reference with a coverageData >= 11X There is a 1.73% of reference with a coverageData >= 12X There is a 1.43% of reference with a coverageData >= 13X There is a 1.21% of reference with a coverageData >= 14X There is a 1.03% of reference with a coverageData >= 15X There is a 0.89% of reference with a coverageData >= 16X There is a 0.78% of reference with a coverageData >= 17X There is a 0.69% of reference with a coverageData >= 18X There is a 0.61% of reference with a coverageData >= 19X There is a 0.55% of reference with a coverageData >= 20X There is a 0.49% of reference with a coverageData >= 21X There is a 0.45% of reference with a coverageData >= 22X There is a 0.41% of reference with a coverageData >= 23X There is a 0.38% of reference with a coverageData >= 24X There is a 0.35% of reference with a coverageData >= 25X There is a 0.33% of reference with a coverageData >= 26X There is a 0.3% of reference with a coverageData >= 27X There is a 0.28% of reference with a coverageData >= 28X There is a 0.27% of reference with a coverageData >= 29X There is a 0.25% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 146096273 1.62974104293616 4.992851158999618 PGA_scaffold2__36_contigs__length_69596280 69596280 116059471 1.6676102659509962 7.233040490350994 PGA_scaffold3__111_contigs__length_57743597 57743597 91223352 1.5798003023607967 5.066126611297191 PGA_scaffold4__129_contigs__length_65288255 65288255 97320849 1.4906333306044097 7.333504072164503 PGA_scaffold5__109_contigs__length_67248332 67248332 89291610 1.3277892156492446 5.304855071099833 PGA_scaffold6__104_contigs__length_61759565 61759565 88047332 1.4256468937240734 7.20622250528409 PGA_scaffold7__69_contigs__length_43120122 43120122 63760935 1.4786816929692361 4.655203009735438 PGA_scaffold8__63_contigs__length_61151155 61151155 93657332 1.5315709408922857 5.5452757818994645 PGA_scaffold9__45_contigs__length_38581958 38581958 65563375 1.6993273125226045 13.977844489559695 PGA_scaffold10__49_contigs__length_53961475 53961475 77319659 1.4328677820611835 4.318084276291675 PGA_scaffold11__79_contigs__length_51449921 51449921 67685380 1.3155584825873687 5.545320151867712 PGA_scaffold12__71_contigs__length_50438331 50438331 81577110 1.6173633897600617 6.508024804345159 PGA_scaffold13__52_contigs__length_44396874 44396874 66916986 1.5072454425507527 5.913668763421352 PGA_scaffold14__91_contigs__length_45393038 45393038 87172660 1.9203971322650844 23.13165985617302 PGA_scaffold15__101_contigs__length_47938513 47938513 60191138 1.2555904268453217 4.77167105157917 PGA_scaffold16__33_contigs__length_31980953 31980953 51774378 1.6189129198244967 13.831163654369519 PGA_scaffold17__51_contigs__length_34923512 34923512 52920885 1.515336859591899 5.198413338916557 PGA_scaffold18__69_contigs__length_27737463 27737463 38080222 1.3728804973980497 8.193619774322105