BamQC report ----------------------------------- >>>>>>> Input bam file = CF06-CM01-Zygote.deduplicated.sorted.bam outfile = CF06-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 = 9,010,546 number of mapped reads = 9,010,546 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,505,273 number of mapped paired reads (second in pair) = 4,505,273 number of mapped paired reads (both in pair) = 9,010,546 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 4,499,196 number of mapped bases = 845,722,300 bp number of sequenced bases = 844,274,244 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,014,808 duplication rate = 39.32% >>>>>>> Insert size mean insert size = 97.8563 std insert size = 40.7897 median insert size = 91 >>>>>>> Mapping quality mean mapping quality = 13.7869 >>>>>>> ACTG content number of A's = 330,312,996 bp (39.12%) number of C's = 90,642,137 bp (10.74%) number of T's = 333,968,403 bp (39.56%) number of G's = 89,345,338 bp (10.58%) number of N's = 5,370 bp (0%) GC percentage = 21.32% >>>>>>> Mismatches and indels general error rate = 0.1621 number of mismatches = 136,108,440 number of insertions = 688,690 mapped reads with insertion percentage = 7.4% number of deletions = 1,063,308 mapped reads with deletion percentage = 11.31% homopolymer indels = 43.45% >>>>>>> Coverage mean coverageData = 1.2351X std coverageData = 3.3811X paired-end adapted mean coverage = 0.643X There is a 29.86% of reference with a coverageData >= 1X There is a 28.33% of reference with a coverageData >= 2X There is a 13.83% of reference with a coverageData >= 3X There is a 12.9% of reference with a coverageData >= 4X There is a 7.2% of reference with a coverageData >= 5X There is a 6.64% of reference with a coverageData >= 6X There is a 4.06% of reference with a coverageData >= 7X There is a 3.72% of reference with a coverageData >= 8X There is a 2.44% of reference with a coverageData >= 9X There is a 2.24% of reference with a coverageData >= 10X There is a 1.55% of reference with a coverageData >= 11X There is a 1.42% of reference with a coverageData >= 12X There is a 1.03% of reference with a coverageData >= 13X There is a 0.95% of reference with a coverageData >= 14X There is a 0.72% of reference with a coverageData >= 15X There is a 0.66% of reference with a coverageData >= 16X There is a 0.52% of reference with a coverageData >= 17X There is a 0.48% of reference with a coverageData >= 18X There is a 0.38% of reference with a coverageData >= 19X There is a 0.36% of reference with a coverageData >= 20X There is a 0.29% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.17% of reference with a coverageData >= 26X There is a 0.15% of reference with a coverageData >= 27X There is a 0.14% 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 0.1% of reference with a coverageData >= 31X There is a 0.09% of reference with a coverageData >= 32X There is a 0.08% of reference with a coverageData >= 33X There is a 0.08% of reference with a coverageData >= 34X There is a 0.07% 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 0.05% 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 0.04% 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 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_035780.1 65668440 92384120 1.4068267801092884 3.174948028769201 NC_035781.1 61752955 96777662 1.567174591078273 3.5098306286474497 NC_035782.1 77061148 110731306 1.4369278018022777 3.4714712052576773 NC_035783.1 59691872 94037887 1.5753884716498756 3.4141963545220984 NC_035784.1 98698416 161282201 1.6340910780168953 3.5220866828709747 NC_035785.1 51258098 46388676 0.9050018984317366 2.683975703694777 NC_035786.1 57830854 52763330 0.9123733500459806 2.478523228163002 NC_035787.1 75944018 68626448 0.9036452087641715 2.506540479092562 NC_035788.1 104168038 90423278 0.8680520410684898 2.576691832401318 NC_035789.1 32650045 28166648 0.8626832826723516 2.5070171282038065 NC_007175.2 17244 4140744 240.1266527487822 153.12493104977213