BamQC report ----------------------------------- >>>>>>> Input bam file = EF08-EM03-Larvae.deduplicated.sorted.bam outfile = EF08-EM03-Larvae/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 17,803,808 number of mapped reads = 17,803,808 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,901,904 number of mapped paired reads (second in pair) = 8,901,904 number of mapped paired reads (both in pair) = 17,803,808 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 8,759,599 number of mapped bases = 1,810,806,669 bp number of sequenced bases = 1,808,559,427 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,498,881 duplication rate = 42.6% >>>>>>> Insert size mean insert size = 113.9201 std insert size = 59.9432 median insert size = 100 >>>>>>> Mapping quality mean mapping quality = 19.8704 >>>>>>> ACTG content number of A's = 684,457,126 bp (37.85%) number of C's = 219,632,722 bp (12.14%) number of T's = 686,694,019 bp (37.97%) number of G's = 217,765,753 bp (12.04%) number of N's = 9,807 bp (0%) GC percentage = 24.18% >>>>>>> Mismatches and indels general error rate = 0.1965 number of mismatches = 353,900,887 number of insertions = 1,302,945 mapped reads with insertion percentage = 6.95% number of deletions = 1,663,676 mapped reads with deletion percentage = 8.97% homopolymer indels = 46.65% >>>>>>> Coverage mean coverageData = 2.6445X std coverageData = 6.5423X paired-end adapted mean coverage = 1.4685X There is a 39.51% of reference with a coverageData >= 1X There is a 35.15% of reference with a coverageData >= 2X There is a 23.89% of reference with a coverageData >= 3X There is a 21.39% of reference with a coverageData >= 4X There is a 16.29% of reference with a coverageData >= 5X There is a 14.67% of reference with a coverageData >= 6X There is a 11.81% of reference with a coverageData >= 7X There is a 10.69% of reference with a coverageData >= 8X There is a 8.89% of reference with a coverageData >= 9X There is a 8.08% of reference with a coverageData >= 10X There is a 6.88% of reference with a coverageData >= 11X There is a 6.27% of reference with a coverageData >= 12X There is a 5.42% of reference with a coverageData >= 13X There is a 4.96% of reference with a coverageData >= 14X There is a 4.33% of reference with a coverageData >= 15X There is a 3.98% of reference with a coverageData >= 16X There is a 3.51% of reference with a coverageData >= 17X There is a 3.23% of reference with a coverageData >= 18X There is a 2.86% of reference with a coverageData >= 19X There is a 2.64% of reference with a coverageData >= 20X There is a 2.35% of reference with a coverageData >= 21X There is a 2.17% of reference with a coverageData >= 22X There is a 1.95% of reference with a coverageData >= 23X There is a 1.8% of reference with a coverageData >= 24X There is a 1.62% of reference with a coverageData >= 25X There is a 1.5% of reference with a coverageData >= 26X There is a 1.35% of reference with a coverageData >= 27X There is a 1.25% of reference with a coverageData >= 28X There is a 1.13% of reference with a coverageData >= 29X There is a 1.05% of reference with a coverageData >= 30X There is a 0.95% of reference with a coverageData >= 31X There is a 0.88% of reference with a coverageData >= 32X There is a 0.8% of reference with a coverageData >= 33X There is a 0.74% of reference with a coverageData >= 34X There is a 0.67% of reference with a coverageData >= 35X There is a 0.62% of reference with a coverageData >= 36X There is a 0.57% of reference with a coverageData >= 37X There is a 0.53% of reference with a coverageData >= 38X There is a 0.48% of reference with a coverageData >= 39X There is a 0.45% of reference with a coverageData >= 40X There is a 0.41% of reference with a coverageData >= 41X There is a 0.38% of reference with a coverageData >= 42X There is a 0.35% of reference with a coverageData >= 43X There is a 0.32% of reference with a coverageData >= 44X There is a 0.29% of reference with a coverageData >= 45X There is a 0.27% of reference with a coverageData >= 46X There is a 0.25% of reference with a coverageData >= 47X There is a 0.23% of reference with a coverageData >= 48X There is a 0.21% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_035780.1 65668440 206778184 3.1488213211704132 7.1028073436452095 NC_035781.1 61752955 211114931 3.418701679943899 7.848287505927697 NC_035782.1 77061148 237073495 3.0764334707289853 7.24746561262951 NC_035783.1 59691872 203123159 3.402861263925514 7.119970902257094 NC_035784.1 98698416 343749153 3.4828234021506486 7.693425923408511 NC_035785.1 51258098 94718530 1.8478744568321672 5.152007908070351 NC_035786.1 57830854 110208082 1.905696948552757 4.966057268686619 NC_035787.1 75944018 151181946 1.9907024935130506 5.431504983820257 NC_035788.1 104168038 189272303 1.8169901884875665 5.174792367436069 NC_035789.1 32650045 62194523 1.904883224510104 5.392155972626099 NC_007175.2 17244 1392363 80.74478079331942 52.871663652906484