BamQC report ----------------------------------- >>>>>>> Input bam file = CF05-CM05-Zygote.deduplicated.sorted.bam outfile = CF05-CM05-Zygote/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 11,511,062 number of mapped reads = 11,511,062 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,755,531 number of mapped paired reads (second in pair) = 5,755,531 number of mapped paired reads (both in pair) = 11,511,062 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 5,735,807 number of mapped bases = 1,130,526,975 bp number of sequenced bases = 1,128,437,592 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,924,615 duplication rate = 38.25% >>>>>>> Insert size mean insert size = 104.4134 std insert size = 45.942 median insert size = 95 >>>>>>> Mapping quality mean mapping quality = 15.9603 >>>>>>> ACTG content number of A's = 430,006,737 bp (38.11%) number of C's = 133,138,924 bp (11.8%) number of T's = 433,751,287 bp (38.44%) number of G's = 131,533,746 bp (11.66%) number of N's = 6,898 bp (0%) GC percentage = 23.45% >>>>>>> Mismatches and indels general error rate = 0.1798 number of mismatches = 202,005,750 number of insertions = 841,995 mapped reads with insertion percentage = 7.04% number of deletions = 1,574,585 mapped reads with deletion percentage = 12.95% homopolymer indels = 45.09% >>>>>>> Coverage mean coverageData = 1.651X std coverageData = 5.6351X paired-end adapted mean coverage = 0.8759X There is a 34.01% of reference with a coverageData >= 1X There is a 31.64% of reference with a coverageData >= 2X There is a 18.23% of reference with a coverageData >= 3X There is a 16.75% of reference with a coverageData >= 4X There is a 10.9% of reference with a coverageData >= 5X There is a 9.93% of reference with a coverageData >= 6X There is a 6.87% of reference with a coverageData >= 7X There is a 6.23% of reference with a coverageData >= 8X There is a 4.48% of reference with a coverageData >= 9X There is a 4.04% of reference with a coverageData >= 10X There is a 2.99% of reference with a coverageData >= 11X There is a 2.69% of reference with a coverageData >= 12X There is a 2.03% of reference with a coverageData >= 13X There is a 1.82% of reference with a coverageData >= 14X There is a 1.4% of reference with a coverageData >= 15X There is a 1.26% of reference with a coverageData >= 16X There is a 0.98% of reference with a coverageData >= 17X There is a 0.88% of reference with a coverageData >= 18X There is a 0.69% of reference with a coverageData >= 19X There is a 0.62% of reference with a coverageData >= 20X There is a 0.5% of reference with a coverageData >= 21X There is a 0.45% of reference with a coverageData >= 22X There is a 0.36% of reference with a coverageData >= 23X There is a 0.33% of reference with a coverageData >= 24X There is a 0.27% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.16% of reference with a coverageData >= 29X There is a 0.14% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.07% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% 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 126509538 1.9264891628307297 3.9229874937136677 NC_035781.1 61752955 130496038 2.113195036577602 4.37271999199053 NC_035782.1 77061148 148409384 1.9258652103132436 4.106865478829704 NC_035783.1 59691872 128029031 2.1448318960410555 4.258377163400229 NC_035784.1 98698416 216811195 2.196703896443485 4.295444758962161 NC_035785.1 51258098 59267903 1.1562641867827401 3.197184140672536 NC_035786.1 57830854 67610354 1.1691052323038493 2.9840249054783734 NC_035787.1 75944018 90423255 1.1906567150555558 3.0241629924345927 NC_035788.1 104168038 113533632 1.089908518772332 2.963546235036924 NC_035789.1 32650045 36464089 1.1168158880026047 2.945389158159419 NC_007175.2 17244 12972556 752.2938993273023 387.4227250913912