BamQC report ----------------------------------- >>>>>>> Input bam file = EF03-EM04-Larvae.deduplicated.sorted.bam outfile = EF03-EM04-Larvae/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 11,668,670 number of mapped reads = 11,668,670 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,834,335 number of mapped paired reads (second in pair) = 5,834,335 number of mapped paired reads (both in pair) = 11,668,670 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 5,807,308 number of mapped bases = 1,175,792,149 bp number of sequenced bases = 1,173,508,610 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,813,911 duplication rate = 37.28% >>>>>>> Insert size mean insert size = 107.8819 std insert size = 47.634 median insert size = 99 >>>>>>> Mapping quality mean mapping quality = 15.4382 >>>>>>> ACTG content number of A's = 444,505,592 bp (37.88%) number of C's = 141,524,921 bp (12.06%) number of T's = 447,826,932 bp (38.16%) number of G's = 139,643,913 bp (11.9%) number of N's = 7,252 bp (0%) GC percentage = 23.96% >>>>>>> Mismatches and indels general error rate = 0.1831 number of mismatches = 213,875,986 number of insertions = 902,969 mapped reads with insertion percentage = 7.43% number of deletions = 1,707,139 mapped reads with deletion percentage = 13.79% homopolymer indels = 43.88% >>>>>>> Coverage mean coverageData = 1.7171X std coverageData = 3.9543X paired-end adapted mean coverage = 0.9169X There is a 35.45% of reference with a coverageData >= 1X There is a 32.82% of reference with a coverageData >= 2X There is a 19.23% of reference with a coverageData >= 3X There is a 17.54% of reference with a coverageData >= 4X There is a 11.56% of reference with a coverageData >= 5X There is a 10.45% of reference with a coverageData >= 6X There is a 7.34% of reference with a coverageData >= 7X There is a 6.59% of reference with a coverageData >= 8X There is a 4.82% of reference with a coverageData >= 9X There is a 4.3% of reference with a coverageData >= 10X There is a 3.22% of reference with a coverageData >= 11X There is a 2.87% of reference with a coverageData >= 12X There is a 2.19% of reference with a coverageData >= 13X There is a 1.94% of reference with a coverageData >= 14X There is a 1.51% of reference with a coverageData >= 15X There is a 1.33% of reference with a coverageData >= 16X There is a 1.04% of reference with a coverageData >= 17X There is a 0.92% of reference with a coverageData >= 18X There is a 0.73% of reference with a coverageData >= 19X There is a 0.65% of reference with a coverageData >= 20X There is a 0.52% of reference with a coverageData >= 21X There is a 0.46% of reference with a coverageData >= 22X There is a 0.37% of reference with a coverageData >= 23X There is a 0.33% of reference with a coverageData >= 24X There is a 0.27% of reference with a coverageData >= 25X There is a 0.24% 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 0.15% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.09% of reference with a coverageData >= 33X There is a 0.08% of reference with a coverageData >= 34X There is a 0.07% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_035780.1 65668440 131870101 2.0081198974728194 4.5079274783713155 NC_035781.1 61752955 137362552 2.224388322793622 4.480652023982546 NC_035782.1 77061148 153816759 1.9960351356302142 4.290751593060369 NC_035783.1 59691872 130682522 2.189285033647462 4.137304035672978 NC_035784.1 98698416 226282008 2.292660988601884 4.644476292025522 NC_035785.1 51258098 63828080 1.2452291928584631 3.234696518067836 NC_035786.1 57830854 71720606 1.2401789190247823 3.046511673089272 NC_035787.1 75944018 96176380 1.2664115296085598 3.1824784301412485 NC_035788.1 104168038 121881483 1.170046833367448 3.040559491950998 NC_035789.1 32650045 40243710 1.2325774742423785 3.1813481576340243 NC_007175.2 17244 1927948 111.80398979355138 62.63455840083897