BamQC report ----------------------------------- >>>>>>> Input bam file = EF07-EM01-Zygote.deduplicated.sorted.bam outfile = EF07-EM01-Zygote/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 5,632,404 number of mapped reads = 5,632,404 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,816,202 number of mapped paired reads (second in pair) = 2,816,202 number of mapped paired reads (both in pair) = 5,632,404 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 2,803,367 number of mapped bases = 486,775,578 bp number of sequenced bases = 486,071,665 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,871,358 duplication rate = 41.49% >>>>>>> Insert size mean insert size = 90.9028 std insert size = 43.9673 median insert size = 81 >>>>>>> Mapping quality mean mapping quality = 17.5013 >>>>>>> ACTG content number of A's = 195,796,561 bp (40.28%) number of C's = 46,552,161 bp (9.58%) number of T's = 197,713,007 bp (40.68%) number of G's = 46,007,125 bp (9.47%) number of N's = 2,811 bp (0%) GC percentage = 19.04% >>>>>>> Mismatches and indels general error rate = 0.1691 number of mismatches = 81,704,073 number of insertions = 413,646 mapped reads with insertion percentage = 7.08% number of deletions = 521,521 mapped reads with deletion percentage = 8.95% homopolymer indels = 46.52% >>>>>>> Coverage mean coverageData = 0.7109X std coverageData = 2.1349X paired-end adapted mean coverage = 0.3724X There is a 22.9% of reference with a coverageData >= 1X There is a 21.35% of reference with a coverageData >= 2X There is a 7.92% of reference with a coverageData >= 3X There is a 7.21% of reference with a coverageData >= 4X There is a 3.03% of reference with a coverageData >= 5X There is a 2.72% of reference with a coverageData >= 6X There is a 1.27% of reference with a coverageData >= 7X There is a 1.13% of reference with a coverageData >= 8X There is a 0.58% of reference with a coverageData >= 9X There is a 0.51% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_035780.1 65668440 53818618 0.8195507309142718 1.9027734925619917 NC_035781.1 61752955 55966356 0.9062943789491531 1.9841878480284254 NC_035782.1 77061148 62959149 0.8170024796412324 1.9468098294576377 NC_035783.1 59691872 53936989 0.9035901738849805 2.0549315135519746 NC_035784.1 98698416 93531573 0.9476501932918558 2.1154181868203366 NC_035785.1 51258098 26110906 0.5094006024179828 1.6163891373846073 NC_035786.1 57830854 29695739 0.5134930049623684 1.6808475451129958 NC_035787.1 75944018 39495609 0.5200621463036101 1.4668395985228146 NC_035788.1 104168038 51356275 0.49301374957258964 1.5210001076758226 NC_035789.1 32650045 16503731 0.5054734534056539 1.5940086306194643 NC_007175.2 17244 3400633 197.2067385757365 102.25794005819665