BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_5.deduplicated.sorted.bam outfile = zr3644_5/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 44,350,908 number of mapped reads = 44,350,908 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 22,175,454 number of mapped paired reads (second in pair) = 22,175,454 number of mapped paired reads (both in pair) = 44,350,908 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 18,638,892 number of mapped bases = 4,689,712,316 bp number of sequenced bases = 4,668,792,668 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,766,261 duplication rate = 13.95% >>>>>>> Insert size mean insert size = 162.0556 std insert size = 71.3163 median insert size = 140 >>>>>>> Mapping quality mean mapping quality = 24.2642 >>>>>>> ACTG content number of A's = 1,915,969,054 bp (41.04%) number of C's = 411,623,091 bp (8.82%) number of T's = 1,934,700,044 bp (41.44%) number of G's = 406,468,189 bp (8.71%) number of N's = 32,290 bp (0%) GC percentage = 17.52% >>>>>>> Mismatches and indels general error rate = 0.1952 number of mismatches = 888,363,435 number of insertions = 9,955,772 mapped reads with insertion percentage = 16.98% number of deletions = 8,907,166 mapped reads with deletion percentage = 16.61% homopolymer indels = 48.88% >>>>>>> Coverage mean coverageData = 8.3153X std coverageData = 9.0706X paired-end adapted mean coverage = 5.9512X There is a 82.9% of reference with a coverageData >= 1X There is a 76.57% of reference with a coverageData >= 2X There is a 70.02% of reference with a coverageData >= 3X There is a 64.48% of reference with a coverageData >= 4X There is a 58.95% of reference with a coverageData >= 5X There is a 53.77% of reference with a coverageData >= 6X There is a 48.73% of reference with a coverageData >= 7X There is a 43.97% of reference with a coverageData >= 8X There is a 39.45% of reference with a coverageData >= 9X There is a 35.22% of reference with a coverageData >= 10X There is a 31.27% of reference with a coverageData >= 11X There is a 27.63% of reference with a coverageData >= 12X There is a 24.29% of reference with a coverageData >= 13X There is a 21.27% of reference with a coverageData >= 14X There is a 18.55% of reference with a coverageData >= 15X There is a 16.11% of reference with a coverageData >= 16X There is a 13.95% of reference with a coverageData >= 17X There is a 12.05% of reference with a coverageData >= 18X There is a 10.38% of reference with a coverageData >= 19X There is a 8.93% of reference with a coverageData >= 20X There is a 7.68% of reference with a coverageData >= 21X There is a 6.6% of reference with a coverageData >= 22X There is a 5.68% of reference with a coverageData >= 23X There is a 4.89% of reference with a coverageData >= 24X There is a 4.22% of reference with a coverageData >= 25X There is a 3.66% of reference with a coverageData >= 26X There is a 3.18% of reference with a coverageData >= 27X There is a 2.77% of reference with a coverageData >= 28X There is a 2.43% of reference with a coverageData >= 29X There is a 2.14% of reference with a coverageData >= 30X There is a 1.9% of reference with a coverageData >= 31X There is a 1.69% of reference with a coverageData >= 32X There is a 1.51% of reference with a coverageData >= 33X There is a 1.36% of reference with a coverageData >= 34X There is a 1.23% of reference with a coverageData >= 35X There is a 1.11% of reference with a coverageData >= 36X There is a 1.01% of reference with a coverageData >= 37X There is a 0.93% of reference with a coverageData >= 38X There is a 0.85% of reference with a coverageData >= 39X There is a 0.78% of reference with a coverageData >= 40X There is a 0.72% of reference with a coverageData >= 41X There is a 0.67% of reference with a coverageData >= 42X There is a 0.62% of reference with a coverageData >= 43X There is a 0.58% of reference with a coverageData >= 44X There is a 0.54% of reference with a coverageData >= 45X There is a 0.5% of reference with a coverageData >= 46X There is a 0.47% of reference with a coverageData >= 47X There is a 0.44% of reference with a coverageData >= 48X There is a 0.41% of reference with a coverageData >= 49X There is a 0.39% of reference with a coverageData >= 50X There is a 0.36% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 483841706 6.360397040180533 10.244121572037779 NC_088854.1 61469542 579477946 9.42707440377545 8.77891506752299 NC_088855.1 61039741 576017931 9.4367689240359 8.597738573364524 NC_088856.1 57946171 432974161 7.47200640746392 9.053791840995407 NC_088857.1 57274926 520923802 9.09514578857771 8.616103286426798 NC_088858.1 56905015 538254309 9.458820263908198 8.51972836127291 NC_088859.1 53672946 525523740 9.791222192275416 8.998626377174945 NC_088860.1 51133819 435577065 8.518375382836162 9.127801580192944 NC_088861.1 50364239 322687155 6.407069011804189 8.392763633548682 NC_088862.1 37310742 271664532 7.281134532248112 8.814922633248711 NW_027062568.1 15579 112019 7.190384491944284 6.519165691274911 NW_027062569.1 16498 107773 6.532488786519578 13.63265575442379 NW_027062570.1 4000 47886 11.9715 13.3060249135495 NW_027062571.1 36893 5105 0.138373133114683 0.6623101938731919 NW_027062572.1 51000 32435 0.6359803921568628 1.5745929427663068 NW_027062573.1 2000 41872 20.936 11.79383533885394 NW_027062574.1 37061 3022 0.08154124281589811 0.4576267515973207 NW_027062575.1 49428 319048 6.454802945698794 11.405887106268647 NW_027062576.1 49232 152538 3.098350666233344 5.794384842116303 NW_027062577.1 17087 117835 6.896178381225493 4.8307269161256885 NW_027062578.1 34507 408199 11.829454893210073 6.781774315568198 NW_027062579.1 64000 341096 5.329625 7.4917324861831025 NW_027062580.1 24229 187521 7.739527013083495 7.238181870886301 NW_027062581.1 5000 13661 2.7322 6.7826480698912865 NW_027062582.1 18808 31839 1.6928434708634623 3.1178413223801487 NW_027062583.1 1000 229 0.229 0.42018924307982947 NW_027062584.1 74000 16881 0.2281216216216216 1.4129039290059457 NW_027062585.1 39334 185141 4.706894798393248 4.575276014691712 NW_027062586.1 258015 645869 2.5032226808518883 5.186225103724936