BamQC report ----------------------------------- >>>>>>> Input bam file = EF03-EM05-Larvae.deduplicated.sorted.bam outfile = EF03-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 = 10,362,584 number of mapped reads = 10,362,584 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,181,292 number of mapped paired reads (second in pair) = 5,181,292 number of mapped paired reads (both in pair) = 10,362,584 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 5,124,658 number of mapped bases = 1,099,552,791 bp number of sequenced bases = 1,097,766,299 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,079,780 duplication rate = 33.63% >>>>>>> Insert size mean insert size = 117.6916 std insert size = 55.3239 median insert size = 106 >>>>>>> Mapping quality mean mapping quality = 14.8508 >>>>>>> ACTG content number of A's = 416,813,801 bp (37.97%) number of C's = 131,431,594 bp (11.97%) number of T's = 419,748,650 bp (38.24%) number of G's = 129,766,128 bp (11.82%) number of N's = 6,126 bp (0%) GC percentage = 23.79% >>>>>>> Mismatches and indels general error rate = 0.187 number of mismatches = 204,303,648 number of insertions = 870,180 mapped reads with insertion percentage = 8.06% number of deletions = 1,313,715 mapped reads with deletion percentage = 12.07% homopolymer indels = 43.7% >>>>>>> Coverage mean coverageData = 1.6058X std coverageData = 3.8241X paired-end adapted mean coverage = 0.8864X There is a 34.51% of reference with a coverageData >= 1X There is a 30.72% of reference with a coverageData >= 2X There is a 18.16% of reference with a coverageData >= 3X There is a 15.93% of reference with a coverageData >= 4X There is a 10.73% of reference with a coverageData >= 5X There is a 9.37% of reference with a coverageData >= 6X There is a 6.75% of reference with a coverageData >= 7X There is a 5.88% of reference with a coverageData >= 8X There is a 4.41% of reference with a coverageData >= 9X There is a 3.83% of reference with a coverageData >= 10X There is a 2.95% of reference with a coverageData >= 11X There is a 2.57% of reference with a coverageData >= 12X There is a 2.02% of reference with a coverageData >= 13X There is a 1.76% of reference with a coverageData >= 14X There is a 1.4% of reference with a coverageData >= 15X There is a 1.22% of reference with a coverageData >= 16X There is a 0.98% of reference with a coverageData >= 17X There is a 0.86% of reference with a coverageData >= 18X There is a 0.7% of reference with a coverageData >= 19X There is a 0.61% of reference with a coverageData >= 20X There is a 0.51% of reference with a coverageData >= 21X There is a 0.45% 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 0.21% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.16% of reference with a coverageData >= 29X There is a 0.14% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.07% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% 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 0.04% of reference with a coverageData >= 43X There is a 0.04% 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 0.03% of reference with a coverageData >= 48X There is a 0.03% 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 122132087 1.85982927263081 3.9632073849050093 NC_035781.1 61752955 127110859 2.0583769473055984 4.521199287939749 NC_035782.1 77061148 143936848 1.8678264175353319 4.258343978760402 NC_035783.1 59691872 123443905 2.068018657548552 4.1127392278222406 NC_035784.1 98698416 209984223 2.127533870452389 4.341499206112657 NC_035785.1 51258098 58910000 1.1492818168945715 3.0984958370923956 NC_035786.1 57830854 67106839 1.160398547806332 3.02529510499809 NC_035787.1 75944018 90428959 1.1907318230120507 3.105955453874433 NC_035788.1 104168038 118025099 1.1330260343388632 3.145663421610878 NC_035789.1 32650045 36775633 1.126357804407314 3.075476668285185 NC_007175.2 17244 1698339 98.48869171885873 63.5893329134521