BamQC report ----------------------------------- >>>>>>> Input bam file = EF01-EM01-Zygote.deduplicated.sorted.bam outfile = EF01-EM01-Zygote/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 6,795,976 number of mapped reads = 6,795,976 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,397,988 number of mapped paired reads (second in pair) = 3,397,988 number of mapped paired reads (both in pair) = 6,795,976 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 3,369,763 number of mapped bases = 693,792,290 bp number of sequenced bases = 692,677,420 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,971,830 duplication rate = 33.61% >>>>>>> Insert size mean insert size = 111.6717 std insert size = 53.0366 median insert size = 101 >>>>>>> Mapping quality mean mapping quality = 13.766 >>>>>>> ACTG content number of A's = 265,992,733 bp (38.4%) number of C's = 79,617,985 bp (11.49%) number of T's = 268,678,044 bp (38.79%) number of G's = 78,384,950 bp (11.32%) number of N's = 3,708 bp (0%) GC percentage = 22.81% >>>>>>> Mismatches and indels general error rate = 0.1695 number of mismatches = 116,738,878 number of insertions = 576,354 mapped reads with insertion percentage = 8.16% number of deletions = 797,531 mapped reads with deletion percentage = 11.23% homopolymer indels = 42.93% >>>>>>> Coverage mean coverageData = 1.0132X std coverageData = 3.9307X paired-end adapted mean coverage = 0.552X There is a 27.71% of reference with a coverageData >= 1X There is a 24.64% of reference with a coverageData >= 2X There is a 11.71% of reference with a coverageData >= 3X There is a 10.15% of reference with a coverageData >= 4X There is a 5.63% of reference with a coverageData >= 5X There is a 4.82% of reference with a coverageData >= 6X There is a 2.96% of reference with a coverageData >= 7X There is a 2.52% of reference with a coverageData >= 8X There is a 1.67% of reference with a coverageData >= 9X There is a 1.43% of reference with a coverageData >= 10X There is a 1% of reference with a coverageData >= 11X There is a 0.87% of reference with a coverageData >= 12X There is a 0.64% of reference with a coverageData >= 13X There is a 0.55% of reference with a coverageData >= 14X There is a 0.43% of reference with a coverageData >= 15X There is a 0.37% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.19% of reference with a coverageData >= 20X There is a 0.16% of reference with a coverageData >= 21X There is a 0.15% of reference with a coverageData >= 22X There is a 0.13% of reference with a coverageData >= 23X There is a 0.12% of reference with a coverageData >= 24X There is a 0.1% of reference with a coverageData >= 25X There is a 0.09% of reference with a coverageData >= 26X There is a 0.08% of reference with a coverageData >= 27X There is a 0.08% of reference with a coverageData >= 28X There is a 0.07% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.06% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.04% of reference with a coverageData >= 35X There is a 0.04% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_035780.1 65668440 74854940 1.1398921612878272 2.6485192144878633 NC_035781.1 61752955 79623524 1.2893880786757492 2.9371707157154034 NC_035782.1 77061148 90355794 1.1725207363897563 2.804954250863233 NC_035783.1 59691872 77777205 1.3029781508611424 2.8643830155425247 NC_035784.1 98698416 131952019 1.3369213443101255 2.957918220983865 NC_035785.1 51258098 36496220 0.7120088615071125 2.178608443240031 NC_035786.1 57830854 42436580 0.7338051760397659 2.0456775048704934 NC_035787.1 75944018 56088776 0.7385542334618113 2.0597323949682163 NC_035788.1 104168038 72692364 0.6978375075087812 2.1099572390699723 NC_035789.1 32650045 23528455 0.7206254999035989 2.078729323078487 NC_007175.2 17244 7986413 463.14155648341455 380.2318017868958