BamQC report ----------------------------------- >>>>>>> Input bam file = EF05-EM05-Zygote.deduplicated.sorted.bam outfile = EF05-EM05-Zygote/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 2,056,578 number of mapped reads = 2,056,578 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,028,289 number of mapped paired reads (second in pair) = 1,028,289 number of mapped paired reads (both in pair) = 2,056,578 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 1,026,620 number of mapped bases = 133,973,611 bp number of sequenced bases = 133,815,505 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 659,021 duplication rate = 43.64% >>>>>>> Insert size mean insert size = 66.292 std insert size = 26.5855 median insert size = 62 >>>>>>> Mapping quality mean mapping quality = 17.6439 >>>>>>> ACTG content number of A's = 53,759,304 bp (40.17%) number of C's = 12,817,813 bp (9.58%) number of T's = 54,584,108 bp (40.79%) number of G's = 12,653,333 bp (9.46%) number of N's = 947 bp (0%) GC percentage = 19.03% >>>>>>> Mismatches and indels general error rate = 0.1803 number of mismatches = 24,027,051 number of insertions = 94,149 mapped reads with insertion percentage = 4.51% number of deletions = 127,980 mapped reads with deletion percentage = 6.12% homopolymer indels = 45.94% >>>>>>> Coverage mean coverageData = 0.1957X std coverageData = 0.8406X paired-end adapted mean coverage = 0.0993X There is a 8.12% of reference with a coverageData >= 1X There is a 7.93% of reference with a coverageData >= 2X There is a 1.29% of reference with a coverageData >= 3X There is a 1.25% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% 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 14957322 0.2277703262023584 0.7841019188183118 NC_035781.1 61752955 15339766 0.24840537590468342 0.850623525329509 NC_035782.1 77061148 17413111 0.22596485326172405 0.8104456178024833 NC_035783.1 59691872 15020064 0.25162662012007264 0.85237240177976 NC_035784.1 98698416 25792382 0.2613251868196142 0.8602531582451016 NC_035785.1 51258098 7168517 0.13985140455270112 0.6470965976138099 NC_035786.1 57830854 8121009 0.1404269250459279 0.6324438619402516 NC_035787.1 75944018 10685327 0.14070004829083443 0.6155380829353757 NC_035788.1 104168038 14105142 0.1354075805862831 0.6122206519227059 NC_035789.1 32650045 4282837 0.13117399991332324 0.6090303554536474 NC_007175.2 17244 1088134 63.102180468568775 46.41897273099632