BamQC report ----------------------------------- >>>>>>> Input bam file = CF07-CM02-Zygote.deduplicated.sorted.bam outfile = CF07-CM02-Zygote/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 7,484,924 number of mapped reads = 7,484,924 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,742,462 number of mapped paired reads (second in pair) = 3,742,462 number of mapped paired reads (both in pair) = 7,484,924 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 3,725,071 number of mapped bases = 683,673,240 bp number of sequenced bases = 682,653,910 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,517,953 duplication rate = 39.61% >>>>>>> Insert size mean insert size = 96.9211 std insert size = 46.3709 median insert size = 87 >>>>>>> Mapping quality mean mapping quality = 17.9296 >>>>>>> ACTG content number of A's = 267,533,509 bp (39.19%) number of C's = 72,924,104 bp (10.68%) number of T's = 270,105,286 bp (39.57%) number of G's = 72,087,340 bp (10.56%) number of N's = 3,671 bp (0%) GC percentage = 21.24% >>>>>>> Mismatches and indels general error rate = 0.174 number of mismatches = 118,142,102 number of insertions = 534,967 mapped reads with insertion percentage = 6.86% number of deletions = 762,628 mapped reads with deletion percentage = 9.77% homopolymer indels = 45.81% >>>>>>> Coverage mean coverageData = 0.9984X std coverageData = 4.3652X paired-end adapted mean coverage = 0.528X There is a 28.03% of reference with a coverageData >= 1X There is a 25.87% of reference with a coverageData >= 2X There is a 11.63% of reference with a coverageData >= 3X There is a 10.52% of reference with a coverageData >= 4X There is a 5.28% of reference with a coverageData >= 5X There is a 4.7% of reference with a coverageData >= 6X There is a 2.55% of reference with a coverageData >= 7X There is a 2.25% of reference with a coverageData >= 8X There is a 1.31% of reference with a coverageData >= 9X There is a 1.15% of reference with a coverageData >= 10X There is a 0.72% of reference with a coverageData >= 11X There is a 0.64% of reference with a coverageData >= 12X There is a 0.43% of reference with a coverageData >= 13X There is a 0.38% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.19% of reference with a coverageData >= 17X There is a 0.17% of reference with a coverageData >= 18X There is a 0.14% of reference with a coverageData >= 19X There is a 0.13% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.1% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% 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 75293951 1.146577427452213 2.4951639721082115 NC_035781.1 61752955 77242585 1.2508322071389135 2.715362889888505 NC_035782.1 77061148 87407786 1.134265297994263 2.572696928677408 NC_035783.1 59691872 75311656 1.2616735491223998 2.603261059919593 NC_035784.1 98698416 129234991 1.3093927566172896 2.7120905173727223 NC_035785.1 51258098 36120597 0.7046807901455883 2.055668355474104 NC_035786.1 57830854 41246210 0.7132215270416031 1.9791283317431079 NC_035787.1 75944018 55196009 0.7267986400192836 1.983545903042034 NC_035788.1 104168038 72660102 0.6975277963860661 1.9782601807392053 NC_035789.1 32650045 22292134 0.6827596715410347 1.9034593964441824 NC_007175.2 17244 11667219 676.5958594293668 283.071410140071