BamQC report ----------------------------------- >>>>>>> Input bam file = CF03-CM03-Zygote.deduplicated.sorted.bam outfile = CF03-CM03-Zygote/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 10,817,182 number of mapped reads = 10,817,182 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,408,591 number of mapped paired reads (second in pair) = 5,408,591 number of mapped paired reads (both in pair) = 10,817,182 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 5,399,246 number of mapped bases = 993,581,701 bp number of sequenced bases = 991,961,969 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,941,213 duplication rate = 41.05% >>>>>>> Insert size mean insert size = 95.8901 std insert size = 41.2864 median insert size = 88 >>>>>>> Mapping quality mean mapping quality = 16.3056 >>>>>>> ACTG content number of A's = 388,198,953 bp (39.13%) number of C's = 106,384,306 bp (10.72%) number of T's = 392,342,570 bp (39.55%) number of G's = 105,030,251 bp (10.59%) number of N's = 5,889 bp (0%) GC percentage = 21.31% >>>>>>> Mismatches and indels general error rate = 0.1616 number of mismatches = 159,382,966 number of insertions = 801,467 mapped reads with insertion percentage = 7.14% number of deletions = 1,220,414 mapped reads with deletion percentage = 10.8% homopolymer indels = 45.38% >>>>>>> Coverage mean coverageData = 1.451X std coverageData = 3.9357X paired-end adapted mean coverage = 0.7563X There is a 31.25% of reference with a coverageData >= 1X There is a 29.64% of reference with a coverageData >= 2X There is a 15.58% of reference with a coverageData >= 3X There is a 14.59% of reference with a coverageData >= 4X There is a 8.77% of reference with a coverageData >= 5X There is a 8.15% of reference with a coverageData >= 6X There is a 5.33% of reference with a coverageData >= 7X There is a 4.94% of reference with a coverageData >= 8X There is a 3.44% of reference with a coverageData >= 9X There is a 3.18% of reference with a coverageData >= 10X There is a 2.33% of reference with a coverageData >= 11X There is a 2.15% of reference with a coverageData >= 12X There is a 1.63% of reference with a coverageData >= 13X There is a 1.51% of reference with a coverageData >= 14X There is a 1.18% of reference with a coverageData >= 15X There is a 1.1% of reference with a coverageData >= 16X There is a 0.88% of reference with a coverageData >= 17X There is a 0.82% of reference with a coverageData >= 18X There is a 0.68% of reference with a coverageData >= 19X There is a 0.63% of reference with a coverageData >= 20X There is a 0.53% of reference with a coverageData >= 21X There is a 0.49% of reference with a coverageData >= 22X There is a 0.42% of reference with a coverageData >= 23X There is a 0.39% of reference with a coverageData >= 24X There is a 0.34% of reference with a coverageData >= 25X There is a 0.32% of reference with a coverageData >= 26X There is a 0.28% of reference with a coverageData >= 27X There is a 0.26% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.14% of reference with a coverageData >= 35X There is a 0.13% of reference with a coverageData >= 36X There is a 0.12% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.07% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_035780.1 65668440 111626253 1.6998462731869373 4.0534003165003885 NC_035781.1 61752955 112183306 1.8166467661345114 4.16460203592808 NC_035782.1 77061148 129849668 1.6850211990093893 4.123977364318897 NC_035783.1 59691872 111193127 1.8627850538847233 4.104766638028572 NC_035784.1 98698416 188569954 1.9105671766809307 4.292834595383232 NC_035785.1 51258098 53806382 1.049714759217168 3.1901138224691867 NC_035786.1 57830854 61144054 1.0572912168995463 2.982146520950637 NC_035787.1 75944018 82711663 1.0891136020746228 3.2010798341234015 NC_035788.1 104168038 106615640 1.0234966698710404 3.1007539102309156 NC_035789.1 32650045 32309888 0.9895817295198215 2.9692293399284093 NC_007175.2 17244 3571766 207.13094409649733 150.48266056973517