BamQC report ----------------------------------- >>>>>>> Input bam file = CF01-CM01-Zygote.deduplicated.sorted.bam outfile = CF01-CM01-Zygote/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 1,297,078 number of mapped reads = 1,297,078 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 648,539 number of mapped paired reads (second in pair) = 648,539 number of mapped paired reads (both in pair) = 1,297,078 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 646,982 number of mapped bases = 122,157,532 bp number of sequenced bases = 121,977,015 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 409,492 duplication rate = 42.95% >>>>>>> Insert size mean insert size = 98.5008 std insert size = 41.8052 median insert size = 91 >>>>>>> Mapping quality mean mapping quality = 15.677 >>>>>>> ACTG content number of A's = 48,585,584 bp (39.83%) number of C's = 12,273,531 bp (10.06%) number of T's = 48,963,022 bp (40.14%) number of G's = 12,153,901 bp (9.96%) number of N's = 977 bp (0%) GC percentage = 20.03% >>>>>>> Mismatches and indels general error rate = 0.1631 number of mismatches = 19,758,429 number of insertions = 111,362 mapped reads with insertion percentage = 8.26% number of deletions = 131,564 mapped reads with deletion percentage = 9.78% homopolymer indels = 44.85% >>>>>>> Coverage mean coverageData = 0.1784X std coverageData = 0.7948X paired-end adapted mean coverage = 0.0931X There is a 7.65% of reference with a coverageData >= 1X There is a 7.07% of reference with a coverageData >= 2X There is a 1.13% of reference with a coverageData >= 3X There is a 1.01% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.22% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_035780.1 65668440 13542754 0.20622926325035285 0.770396599301814 NC_035781.1 61752955 14006125 0.22680898428261448 0.8035805570792802 NC_035782.1 77061148 15930537 0.2067259236781679 0.7616240470519476 NC_035783.1 59691872 13636807 0.2284533311335922 0.8028267705268248 NC_035784.1 98698416 23288595 0.23595713025424847 0.8304916691234133 NC_035785.1 51258098 6575680 0.12828568083037337 0.6331936861701374 NC_035786.1 57830854 7460509 0.12900568613425628 0.6172300511732579 NC_035787.1 75944018 10068548 0.13257855279661396 0.617716770293209 NC_035788.1 104168038 12681151 0.12173744695085838 0.5972667440809093 NC_035789.1 32650045 3997140 0.12242372100865405 0.601950717446968 NC_007175.2 17244 969686 56.23324054743679 39.03481431676783