BamQC report ----------------------------------- >>>>>>> Input bam file = EF03-EM03-Zygote.deduplicated.sorted.bam outfile = EF03-EM03-Zygote/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 5,464,172 number of mapped reads = 5,464,172 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,732,086 number of mapped paired reads (second in pair) = 2,732,086 number of mapped paired reads (both in pair) = 5,464,172 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 2,727,092 number of mapped bases = 499,433,142 bp number of sequenced bases = 498,563,739 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,715,841 duplication rate = 37.7% >>>>>>> Insert size mean insert size = 95.4312 std insert size = 41.5635 median insert size = 88 >>>>>>> Mapping quality mean mapping quality = 14.0685 >>>>>>> ACTG content number of A's = 197,378,137 bp (39.59%) number of C's = 51,118,498 bp (10.25%) number of T's = 199,685,956 bp (40.05%) number of G's = 50,377,070 bp (10.1%) number of N's = 4,078 bp (0%) GC percentage = 20.36% >>>>>>> Mismatches and indels general error rate = 0.1578 number of mismatches = 78,205,858 number of insertions = 424,477 mapped reads with insertion percentage = 7.51% number of deletions = 650,072 mapped reads with deletion percentage = 11.38% homopolymer indels = 44.68% >>>>>>> Coverage mean coverageData = 0.7294X std coverageData = 2.3045X paired-end adapted mean coverage = 0.3802X There is a 21.6% of reference with a coverageData >= 1X There is a 20.27% of reference with a coverageData >= 2X There is a 7.67% of reference with a coverageData >= 3X There is a 7.07% of reference with a coverageData >= 4X There is a 3.34% of reference with a coverageData >= 5X There is a 3.05% of reference with a coverageData >= 6X There is a 1.68% of reference with a coverageData >= 7X There is a 1.54% of reference with a coverageData >= 8X There is a 0.95% of reference with a coverageData >= 9X There is a 0.87% of reference with a coverageData >= 10X There is a 0.59% of reference with a coverageData >= 11X There is a 0.54% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.36% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.2% of reference with a coverageData >= 17X There is a 0.18% of reference with a coverageData >= 18X There is a 0.15% of reference with a coverageData >= 19X There is a 0.14% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.11% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.09% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% 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 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_035780.1 65668440 54101703 0.8238615535864717 2.173920495635293 NC_035781.1 61752955 57332493 0.9284169964012249 2.431048761352214 NC_035782.1 77061148 65647618 0.8518899562721282 2.328097131915398 NC_035783.1 59691872 55526014 0.9302106323621414 2.390903938328431 NC_035784.1 98698416 96366255 0.9763708365897179 2.459213207747504 NC_035785.1 51258098 27100864 0.5287138044021844 1.8984037896912844 NC_035786.1 57830854 31893168 0.5514905244179863 1.901706005342712 NC_035787.1 75944018 40749339 0.5365707539993473 1.7752340138172495 NC_035788.1 104168038 52761443 0.506503184786873 1.776103019190235 NC_035789.1 32650045 15637082 0.47892987590063046 1.6345442532721743 NC_007175.2 17244 2317163 134.37502899559266 113.7093873678615