BamQC report ----------------------------------- >>>>>>> Input bam file = EF02-EM02-Zygote.deduplicated.sorted.bam outfile = EF02-EM02-Zygote/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 10,870,112 number of mapped reads = 10,870,112 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,435,056 number of mapped paired reads (second in pair) = 5,435,056 number of mapped paired reads (both in pair) = 10,870,112 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 5,427,314 number of mapped bases = 935,940,830 bp number of sequenced bases = 934,579,988 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,960,328 duplication rate = 42.63% >>>>>>> Insert size mean insert size = 89.0007 std insert size = 38.5799 median insert size = 82 >>>>>>> Mapping quality mean mapping quality = 17.3632 >>>>>>> ACTG content number of A's = 357,720,748 bp (38.28%) number of C's = 108,200,706 bp (11.58%) number of T's = 361,704,085 bp (38.7%) number of G's = 106,948,695 bp (11.44%) number of N's = 5,754 bp (0%) GC percentage = 23.02% >>>>>>> Mismatches and indels general error rate = 0.195 number of mismatches = 181,558,790 number of insertions = 670,714 mapped reads with insertion percentage = 5.97% number of deletions = 1,038,566 mapped reads with deletion percentage = 9.2% homopolymer indels = 45.1% >>>>>>> Coverage mean coverageData = 1.3669X std coverageData = 4.9X paired-end adapted mean coverage = 0.7053X There is a 29.07% of reference with a coverageData >= 1X There is a 27.81% of reference with a coverageData >= 2X There is a 14.63% of reference with a coverageData >= 3X There is a 13.91% of reference with a coverageData >= 4X There is a 8.51% of reference with a coverageData >= 5X There is a 8.05% of reference with a coverageData >= 6X There is a 5.32% of reference with a coverageData >= 7X There is a 5.02% of reference with a coverageData >= 8X There is a 3.47% of reference with a coverageData >= 9X There is a 3.26% of reference with a coverageData >= 10X There is a 2.33% of reference with a coverageData >= 11X There is a 2.19% of reference with a coverageData >= 12X There is a 1.59% of reference with a coverageData >= 13X There is a 1.49% of reference with a coverageData >= 14X There is a 1.11% of reference with a coverageData >= 15X There is a 1.04% of reference with a coverageData >= 16X There is a 0.78% of reference with a coverageData >= 17X There is a 0.73% of reference with a coverageData >= 18X There is a 0.55% of reference with a coverageData >= 19X There is a 0.52% of reference with a coverageData >= 20X There is a 0.4% of reference with a coverageData >= 21X There is a 0.37% of reference with a coverageData >= 22X There is a 0.29% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.16% of reference with a coverageData >= 27X There is a 0.15% of reference with a coverageData >= 28X There is a 0.12% of reference with a coverageData >= 29X There is a 0.11% of reference with a coverageData >= 30X There is a 0.09% of reference with a coverageData >= 31X There is a 0.08% of reference with a coverageData >= 32X There is a 0.07% of reference with a coverageData >= 33X There is a 0.07% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% 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 0.03% 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 105830214 1.61158410341406 3.687290114962092 NC_035781.1 61752955 109673907 1.7760106702586136 4.147397076713375 NC_035782.1 77061148 124121172 1.6106841803083443 3.834818020290127 NC_035783.1 59691872 105714655 1.7710058582180166 3.782178865180387 NC_035784.1 98698416 183481338 1.8590099561476245 4.2151014410245455 NC_035785.1 51258098 49219995 0.9602384193030339 2.776498141839146 NC_035786.1 57830854 55045362 0.9518338082989403 2.6064052340398756 NC_035787.1 75944018 74953819 0.9869614615334154 2.7640883677927324 NC_035788.1 104168038 89841425 0.8624663258033141 2.586503126856179 NC_035789.1 32650045 27578605 0.8446728021354948 2.621782140882285 NC_007175.2 17244 10480338 607.7672233820459 341.97664215081886