BamQC report ----------------------------------- >>>>>>> Input bam file = CF04-CM04-Zygote.deduplicated.sorted.bam outfile = CF04-CM04-Zygote/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 10,799,432 number of mapped reads = 10,799,432 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,399,716 number of mapped paired reads (second in pair) = 5,399,716 number of mapped paired reads (both in pair) = 10,799,432 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 5,374,806 number of mapped bases = 1,067,662,811 bp number of sequenced bases = 1,065,766,154 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,751,641 duplication rate = 38.36% >>>>>>> Insert size mean insert size = 105.8671 std insert size = 47.8597 median insert size = 96 >>>>>>> Mapping quality mean mapping quality = 16.975 >>>>>>> ACTG content number of A's = 415,940,497 bp (39.03%) number of C's = 116,133,300 bp (10.9%) number of T's = 419,089,148 bp (39.32%) number of G's = 114,597,634 bp (10.75%) number of N's = 5,575 bp (0%) GC percentage = 21.65% >>>>>>> Mismatches and indels general error rate = 0.1708 number of mismatches = 181,071,433 number of insertions = 862,723 mapped reads with insertion percentage = 7.65% number of deletions = 1,426,905 mapped reads with deletion percentage = 12.53% homopolymer indels = 45.95% >>>>>>> Coverage mean coverageData = 1.5592X std coverageData = 4.4844X paired-end adapted mean coverage = 0.8329X There is a 33.81% of reference with a coverageData >= 1X There is a 31.2% of reference with a coverageData >= 2X There is a 17.67% of reference with a coverageData >= 3X There is a 16.06% of reference with a coverageData >= 4X There is a 10.16% of reference with a coverageData >= 5X There is a 9.15% of reference with a coverageData >= 6X There is a 6.17% of reference with a coverageData >= 7X There is a 5.52% of reference with a coverageData >= 8X There is a 3.89% of reference with a coverageData >= 9X There is a 3.47% of reference with a coverageData >= 10X There is a 2.54% of reference with a coverageData >= 11X There is a 2.27% of reference with a coverageData >= 12X There is a 1.7% of reference with a coverageData >= 13X There is a 1.52% of reference with a coverageData >= 14X There is a 1.17% of reference with a coverageData >= 15X There is a 1.05% of reference with a coverageData >= 16X There is a 0.83% of reference with a coverageData >= 17X There is a 0.74% of reference with a coverageData >= 18X There is a 0.6% of reference with a coverageData >= 19X There is a 0.54% of reference with a coverageData >= 20X There is a 0.44% of reference with a coverageData >= 21X There is a 0.4% of reference with a coverageData >= 22X There is a 0.33% of reference with a coverageData >= 23X There is a 0.3% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.16% of reference with a coverageData >= 29X There is a 0.15% of reference with a coverageData >= 30X There is a 0.13% of reference with a coverageData >= 31X There is a 0.12% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.1% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% 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 0.04% 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 116740317 1.7777233173195526 3.637095062977861 NC_035781.1 61752955 123395123 1.9982059643947403 4.107751370069284 NC_035782.1 77061148 139330033 1.8080451254113161 3.976408567967784 NC_035783.1 59691872 118768988 1.989701177406532 3.8741090500868878 NC_035784.1 98698416 205588338 2.082995313724184 4.02479111589954 NC_035785.1 51258098 56978199 1.1115940938737134 3.0199929592151715 NC_035786.1 57830854 64237970 1.110790617064033 2.8818763172595125 NC_035787.1 75944018 87653139 1.154180952079728 2.915314514226442 NC_035788.1 104168038 112574738 1.0807032575577549 2.9919029552271224 NC_035789.1 32650045 33941445 1.0395527785643175 2.8151630862065677 NC_007175.2 17244 8454521 490.28769427047087 256.405189668719