BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-160_S7_L002_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 = 17,984,132 number of mapped reads = 17,984,132 (100%) number of mapped paired reads (first in pair) = 8,992,066 number of mapped paired reads (second in pair) = 8,992,066 number of mapped paired reads (both in pair) = 17,984,132 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,546,252,988 bp number of sequenced bases = 1,542,827,822 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,888,702 duplication rate = 35.37% >>>>>>> Insert size mean insert size = 136.9852 std insert size = 87.2078 median insert size = 113 >>>>>>> Mapping quality mean mapping quality = 24.0295 >>>>>>> ACTG content number of A's = 594,092,691 bp (38.51%) number of C's = 179,012,731 bp (11.6%) number of T's = 592,325,085 bp (38.39%) number of G's = 177,397,315 bp (11.5%) number of N's = 80,217 bp (0.01%) GC percentage = 23.1% >>>>>>> Mismatches and indels general error rate = 0.187 number of mismatches = 282,695,727 number of insertions = 1,934,243 mapped reads with insertion percentage = 9.41% number of deletions = 1,830,654 mapped reads with deletion percentage = 9.23% homopolymer indels = 48.84% >>>>>>> Coverage mean coverageData = 1.6408X std coverageData = 9.7083X There is a 39.28% of reference with a coverageData >= 1X There is a 27.28% of reference with a coverageData >= 2X There is a 18.19% of reference with a coverageData >= 3X There is a 13.64% of reference with a coverageData >= 4X There is a 10.03% of reference with a coverageData >= 5X There is a 7.82% of reference with a coverageData >= 6X There is a 6.03% of reference with a coverageData >= 7X There is a 4.82% of reference with a coverageData >= 8X There is a 3.84% of reference with a coverageData >= 9X There is a 3.14% of reference with a coverageData >= 10X There is a 2.56% of reference with a coverageData >= 11X There is a 2.14% of reference with a coverageData >= 12X There is a 1.79% of reference with a coverageData >= 13X There is a 1.52% of reference with a coverageData >= 14X There is a 1.29% of reference with a coverageData >= 15X There is a 1.12% of reference with a coverageData >= 16X There is a 0.97% of reference with a coverageData >= 17X There is a 0.86% of reference with a coverageData >= 18X There is a 0.76% of reference with a coverageData >= 19X There is a 0.68% of reference with a coverageData >= 20X There is a 0.61% of reference with a coverageData >= 21X There is a 0.55% of reference with a coverageData >= 22X There is a 0.5% of reference with a coverageData >= 23X There is a 0.46% of reference with a coverageData >= 24X There is a 0.42% of reference with a coverageData >= 25X There is a 0.39% of reference with a coverageData >= 26X There is a 0.36% of reference with a coverageData >= 27X There is a 0.34% of reference with a coverageData >= 28X There is a 0.32% of reference with a coverageData >= 29X There is a 0.3% of reference with a coverageData >= 30X There is a 0.28% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.12% 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 155236072 1.731697822863646 5.902036008241749 PGA_scaffold2__36_contigs__length_69596280 69596280 124632469 1.790792108428784 7.637256918524707 PGA_scaffold3__111_contigs__length_57743597 57743597 98380192 1.7037420096984952 5.618850379500003 PGA_scaffold4__129_contigs__length_65288255 65288255 104889260 1.6065563400339005 7.658981484706473 PGA_scaffold5__109_contigs__length_67248332 67248332 96841694 1.4400609073842903 5.974800955755179 PGA_scaffold6__104_contigs__length_61759565 61759565 96341459 1.5599439374289634 10.415123227264418 PGA_scaffold7__69_contigs__length_43120122 43120122 69742150 1.617392223519219 5.324956130049458 PGA_scaffold8__63_contigs__length_61151155 61151155 100278754 1.6398505310324882 6.294004983622326 PGA_scaffold9__45_contigs__length_38581958 38581958 70328491 1.8228336415689426 14.266771139251004 PGA_scaffold10__49_contigs__length_53961475 53961475 82316083 1.5254602102703827 4.74586607949452 PGA_scaffold11__79_contigs__length_51449921 51449921 73413126 1.4268851063930692 5.95161002626992 PGA_scaffold12__71_contigs__length_50438331 50438331 87755351 1.7398543778143651 7.3378233816346805 PGA_scaffold13__52_contigs__length_44396874 44396874 72324536 1.62904568461284 6.399710813874458 PGA_scaffold14__91_contigs__length_45393038 45393038 94530694 2.0824932228594175 25.943641445927604 PGA_scaffold15__101_contigs__length_47938513 47938513 64239307 1.3400354533316459 5.2548339210190775 PGA_scaffold16__33_contigs__length_31980953 31980953 55811741 1.7451556556178922 19.75729567933616 PGA_scaffold17__51_contigs__length_34923512 34923512 58725263 1.6815394454028565 6.653293593191495 PGA_scaffold18__69_contigs__length_27737463 27737463 40466346 1.4589058126909444 8.234777507498562