BamQC report ----------------------------------- >>>>>>> Input bam file = EF04-EM05-Larvae.deduplicated.sorted.bam outfile = EF04-EM05-Larvae/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 16,787,080 number of mapped reads = 16,787,080 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,393,540 number of mapped paired reads (second in pair) = 8,393,540 number of mapped paired reads (both in pair) = 16,787,080 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 8,241,199 number of mapped bases = 1,855,973,614 bp number of sequenced bases = 1,853,447,968 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,006,426 duplication rate = 36.43% >>>>>>> Insert size mean insert size = 125.5406 std insert size = 59.8396 median insert size = 112 >>>>>>> Mapping quality mean mapping quality = 18.9642 >>>>>>> ACTG content number of A's = 706,414,715 bp (38.11%) number of C's = 220,089,896 bp (11.87%) number of T's = 708,788,717 bp (38.24%) number of G's = 218,144,800 bp (11.77%) number of N's = 9,840 bp (0%) GC percentage = 23.64% >>>>>>> Mismatches and indels general error rate = 0.1962 number of mismatches = 362,125,841 number of insertions = 1,373,557 mapped reads with insertion percentage = 7.75% number of deletions = 1,857,044 mapped reads with deletion percentage = 10.58% homopolymer indels = 46.27% >>>>>>> Coverage mean coverageData = 2.7105X std coverageData = 6.598X paired-end adapted mean coverage = 1.5267X There is a 41.01% of reference with a coverageData >= 1X There is a 36.38% of reference with a coverageData >= 2X There is a 25.12% of reference with a coverageData >= 3X There is a 22.33% of reference with a coverageData >= 4X There is a 17.17% of reference with a coverageData >= 5X There is a 15.33% of reference with a coverageData >= 6X There is a 12.41% of reference with a coverageData >= 7X There is a 11.13% of reference with a coverageData >= 8X There is a 9.29% of reference with a coverageData >= 9X There is a 8.37% of reference with a coverageData >= 10X There is a 7.13% of reference with a coverageData >= 11X There is a 6.45% of reference with a coverageData >= 12X There is a 5.57% of reference with a coverageData >= 13X There is a 5.06% of reference with a coverageData >= 14X There is a 4.41% of reference with a coverageData >= 15X There is a 4.02% of reference with a coverageData >= 16X There is a 3.53% of reference with a coverageData >= 17X There is a 3.22% of reference with a coverageData >= 18X There is a 2.85% of reference with a coverageData >= 19X There is a 2.6% of reference with a coverageData >= 20X There is a 2.31% of reference with a coverageData >= 21X There is a 2.11% of reference with a coverageData >= 22X There is a 1.89% of reference with a coverageData >= 23X There is a 1.72% of reference with a coverageData >= 24X There is a 1.54% of reference with a coverageData >= 25X There is a 1.41% of reference with a coverageData >= 26X There is a 1.27% of reference with a coverageData >= 27X There is a 1.16% of reference with a coverageData >= 28X There is a 1.04% of reference with a coverageData >= 29X There is a 0.95% of reference with a coverageData >= 30X There is a 0.86% of reference with a coverageData >= 31X There is a 0.79% of reference with a coverageData >= 32X There is a 0.71% of reference with a coverageData >= 33X There is a 0.65% of reference with a coverageData >= 34X There is a 0.59% of reference with a coverageData >= 35X There is a 0.54% of reference with a coverageData >= 36X There is a 0.49% of reference with a coverageData >= 37X There is a 0.45% of reference with a coverageData >= 38X There is a 0.4% of reference with a coverageData >= 39X There is a 0.37% of reference with a coverageData >= 40X There is a 0.34% of reference with a coverageData >= 41X There is a 0.31% of reference with a coverageData >= 42X There is a 0.28% of reference with a coverageData >= 43X There is a 0.26% of reference with a coverageData >= 44X There is a 0.24% of reference with a coverageData >= 45X There is a 0.22% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_035780.1 65668440 210643108 3.2076764424432804 7.333460331663192 NC_035781.1 61752955 215768079 3.4940526975591695 7.7895082168125045 NC_035782.1 77061148 242074161 3.1413256521950594 7.190383917173809 NC_035783.1 59691872 207796321 3.4811493430797413 7.2620844646010845 NC_035784.1 98698416 350482138 3.5510411636190797 7.677946353228571 NC_035785.1 51258098 99952979 1.9499939112059912 5.2793371211169955 NC_035786.1 57830854 112736048 1.9494100502129883 4.908259849476035 NC_035787.1 75944018 154241709 2.0309922106043956 5.381985650269448 NC_035788.1 104168038 193911131 1.8615223510305532 5.090358464343922 NC_035789.1 32650045 65774597 2.0145331193264817 5.548364847726955 NC_007175.2 17244 2593343 150.39103456274646 82.56957481134278