BamQC report ----------------------------------- >>>>>>> Input bam file = CF08-CM03-Zygote.deduplicated.sorted.bam outfile = CF08-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 = 7,039,202 number of mapped reads = 7,039,202 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,519,601 number of mapped paired reads (second in pair) = 3,519,601 number of mapped paired reads (both in pair) = 7,039,202 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 3,512,728 number of mapped bases = 648,585,799 bp number of sequenced bases = 647,427,991 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,502,554 duplication rate = 39.3% >>>>>>> Insert size mean insert size = 96.487 std insert size = 42.3748 median insert size = 89 >>>>>>> Mapping quality mean mapping quality = 14.3751 >>>>>>> ACTG content number of A's = 261,870,646 bp (40.45%) number of C's = 60,723,607 bp (9.38%) number of T's = 264,997,312 bp (40.93%) number of G's = 59,832,385 bp (9.24%) number of N's = 4,041 bp (0%) GC percentage = 18.62% >>>>>>> Mismatches and indels general error rate = 0.1494 number of mismatches = 96,046,578 number of insertions = 585,562 mapped reads with insertion percentage = 8.01% number of deletions = 867,818 mapped reads with deletion percentage = 11.77% homopolymer indels = 45.67% >>>>>>> Coverage mean coverageData = 0.9472X std coverageData = 3.6343X paired-end adapted mean coverage = 0.4951X There is a 22.68% of reference with a coverageData >= 1X There is a 21.32% of reference with a coverageData >= 2X There is a 9.37% of reference with a coverageData >= 3X There is a 8.69% of reference with a coverageData >= 4X There is a 4.84% of reference with a coverageData >= 5X There is a 4.47% of reference with a coverageData >= 6X There is a 2.88% of reference with a coverageData >= 7X There is a 2.66% of reference with a coverageData >= 8X There is a 1.88% of reference with a coverageData >= 9X There is a 1.75% of reference with a coverageData >= 10X There is a 1.31% of reference with a coverageData >= 11X There is a 1.22% of reference with a coverageData >= 12X There is a 0.96% of reference with a coverageData >= 13X There is a 0.9% of reference with a coverageData >= 14X There is a 0.73% of reference with a coverageData >= 15X There is a 0.68% of reference with a coverageData >= 16X There is a 0.57% of reference with a coverageData >= 17X There is a 0.53% of reference with a coverageData >= 18X There is a 0.45% of reference with a coverageData >= 19X There is a 0.43% of reference with a coverageData >= 20X There is a 0.37% of reference with a coverageData >= 21X There is a 0.35% of reference with a coverageData >= 22X There is a 0.3% of reference with a coverageData >= 23X There is a 0.29% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.15% of reference with a coverageData >= 32X There is a 0.14% of reference with a coverageData >= 33X There is a 0.13% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.08% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.07% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.06% 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 70898167 1.0796383620503243 3.346567711245843 NC_035781.1 61752955 72517995 1.1743242894206438 3.5479224677337897 NC_035782.1 77061148 83140344 1.0788879501250097 3.413801128991595 NC_035783.1 59691872 71393054 1.196026386976103 3.5944727773496634 NC_035784.1 98698416 121296667 1.2289626512344434 3.7473686212662423 NC_035785.1 51258098 35483088 0.6922435553500249 2.7674623288918627 NC_035786.1 57830854 41237126 0.7130644482614765 2.788827981393019 NC_035787.1 75944018 54701324 0.7202848287537276 2.9874405334198695 NC_035788.1 104168038 71873841 0.6899797901540585 2.7000296047302457 NC_035789.1 32650045 21616314 0.6620607720448778 2.589043947481825 NC_007175.2 17244 4427879 256.7779517513338 217.5205309212243