BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-111_S29_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 = 20,933,644 number of mapped reads = 20,933,644 (100%) number of mapped paired reads (first in pair) = 10,466,822 number of mapped paired reads (second in pair) = 10,466,822 number of mapped paired reads (both in pair) = 20,933,644 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,909,924,266 bp number of sequenced bases = 1,905,862,047 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,097,969 duplication rate = 29.51% >>>>>>> Insert size mean insert size = 156.5492 std insert size = 88.4518 median insert size = 134 >>>>>>> Mapping quality mean mapping quality = 25.0252 >>>>>>> ACTG content number of A's = 740,834,461 bp (38.87%) number of C's = 213,196,580 bp (11.19%) number of T's = 739,471,449 bp (38.8%) number of G's = 212,359,557 bp (11.14%) number of N's = 25,695 bp (0%) GC percentage = 22.33% >>>>>>> Mismatches and indels general error rate = 0.1868 number of mismatches = 349,710,683 number of insertions = 2,165,169 mapped reads with insertion percentage = 9.05% number of deletions = 2,170,302 mapped reads with deletion percentage = 9.38% homopolymer indels = 51.39% >>>>>>> Coverage mean coverageData = 2.0268X std coverageData = 7.952X There is a 46.38% of reference with a coverageData >= 1X There is a 33.31% of reference with a coverageData >= 2X There is a 23.69% of reference with a coverageData >= 3X There is a 17.95% of reference with a coverageData >= 4X There is a 13.49% of reference with a coverageData >= 5X There is a 10.5% of reference with a coverageData >= 6X There is a 8.11% of reference with a coverageData >= 7X There is a 6.43% of reference with a coverageData >= 8X There is a 5.07% of reference with a coverageData >= 9X There is a 4.11% of reference with a coverageData >= 10X There is a 3.32% of reference with a coverageData >= 11X There is a 2.75% of reference with a coverageData >= 12X There is a 2.27% of reference with a coverageData >= 13X There is a 1.92% of reference with a coverageData >= 14X There is a 1.61% of reference with a coverageData >= 15X There is a 1.39% of reference with a coverageData >= 16X There is a 1.2% of reference with a coverageData >= 17X There is a 1.05% of reference with a coverageData >= 18X There is a 0.92% of reference with a coverageData >= 19X There is a 0.82% 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 0.59% of reference with a coverageData >= 23X There is a 0.54% of reference with a coverageData >= 24X There is a 0.49% of reference with a coverageData >= 25X There is a 0.45% of reference with a coverageData >= 26X There is a 0.42% of reference with a coverageData >= 27X There is a 0.39% of reference with a coverageData >= 28X There is a 0.36% of reference with a coverageData >= 29X There is a 0.34% of reference with a coverageData >= 30X There is a 0.32% 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 194679434 2.1716985470627397 5.133334600259497 PGA_scaffold2__36_contigs__length_69596280 69596280 153602044 2.207043882230487 6.394153339897212 PGA_scaffold3__111_contigs__length_57743597 57743597 121866655 2.1104791064540023 5.84205281909669 PGA_scaffold4__129_contigs__length_65288255 65288255 133747673 2.0485717224330777 7.331309006173404 PGA_scaffold5__109_contigs__length_67248332 67248332 119227350 1.77294137198823 5.353133853664141 PGA_scaffold6__104_contigs__length_61759565 61759565 117492491 1.9024177226636878 7.093439761932097 PGA_scaffold7__69_contigs__length_43120122 43120122 85752964 1.9886994753864564 5.467041029188133 PGA_scaffold8__63_contigs__length_61151155 61151155 124391221 2.034159796327641 5.963529208993868 PGA_scaffold9__45_contigs__length_38581958 38581958 84226478 2.183053488368838 12.229950060974117 PGA_scaffold10__49_contigs__length_53961475 53961475 101985805 1.8899743752371483 4.690179451947554 PGA_scaffold11__79_contigs__length_51449921 51449921 91719013 1.782685205677964 5.792415426233467 PGA_scaffold12__71_contigs__length_50438331 50438331 109028220 2.161614348420847 7.208855871123904 PGA_scaffold13__52_contigs__length_44396874 44396874 88582152 1.9952339887713717 6.126472393603292 PGA_scaffold14__91_contigs__length_45393038 45393038 115124433 2.5361693791017026 21.5974071275451 PGA_scaffold15__101_contigs__length_47938513 47938513 81056376 1.6908404313667384 5.30109700519351 PGA_scaffold16__33_contigs__length_31980953 31980953 66685102 2.085150558208819 9.201675263125496 PGA_scaffold17__51_contigs__length_34923512 34923512 71728706 2.0538800908682955 5.415669720719302 PGA_scaffold18__69_contigs__length_27737463 27737463 49028149 1.7675787075407725 6.421957839216313