BamQC report ----------------------------------- >>>>>>> Input bam file = EF06-EM06-Larvae.deduplicated.sorted.bam outfile = EF06-EM06-Larvae/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 2,495,062 number of mapped reads = 2,495,062 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,247,531 number of mapped paired reads (second in pair) = 1,247,531 number of mapped paired reads (both in pair) = 2,495,062 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 1,243,653 number of mapped bases = 262,281,545 bp number of sequenced bases = 261,732,789 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 673,503 duplication rate = 33.29% >>>>>>> Insert size mean insert size = 111.8583 std insert size = 44.5478 median insert size = 105 >>>>>>> Mapping quality mean mapping quality = 15.2023 >>>>>>> ACTG content number of A's = 103,496,948 bp (39.54%) number of C's = 27,204,233 bp (10.39%) number of T's = 104,226,688 bp (39.82%) number of G's = 26,802,742 bp (10.24%) number of N's = 2,178 bp (0%) GC percentage = 20.63% >>>>>>> Mismatches and indels general error rate = 0.1635 number of mismatches = 42,539,082 number of insertions = 231,314 mapped reads with insertion percentage = 8.86% number of deletions = 404,162 mapped reads with deletion percentage = 15.22% homopolymer indels = 44.5% >>>>>>> Coverage mean coverageData = 0.383X std coverageData = 1.3946X paired-end adapted mean coverage = 0.2033X There is a 14.96% of reference with a coverageData >= 1X There is a 13.55% of reference with a coverageData >= 2X There is a 3.46% of reference with a coverageData >= 3X There is a 3.01% of reference with a coverageData >= 4X There is a 0.95% of reference with a coverageData >= 5X There is a 0.81% of reference with a coverageData >= 6X There is a 0.31% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.12% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_035780.1 65668440 26397116 0.40197568268714773 1.1086677577933843 NC_035781.1 61752955 27878491 0.4514519345673418 1.1968114011484057 NC_035782.1 77061148 32518430 0.4219821640861099 1.189936108706066 NC_035783.1 59691872 28767083 0.481926299781652 1.2073501612728885 NC_035784.1 98698416 54563909 0.5528346979752947 1.3001255471122388 NC_035785.1 51258098 14857818 0.28986284274535506 0.9838412635692035 NC_035786.1 57830854 16606215 0.28715147453987105 0.9342228712713587 NC_035787.1 75944018 21208300 0.27926228501631295 0.9198454335784155 NC_035788.1 104168038 28008798 0.2688809210364507 0.9470041750879563 NC_035789.1 32650045 8827589 0.27036988769847026 0.8968467789145035 NC_007175.2 17244 2647796 153.54882857805615 78.17707436119419