BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_18.deduplicated.sorted.bam outfile = zr3644_18/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 57,967,116 number of mapped reads = 57,967,116 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 28,983,558 number of mapped paired reads (second in pair) = 28,983,558 number of mapped paired reads (both in pair) = 57,967,116 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 24,585,020 number of mapped bases = 6,086,610,739 bp number of sequenced bases = 6,060,071,371 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,243,680 duplication rate = 17.47% >>>>>>> Insert size mean insert size = 159.5141 std insert size = 70.565 median insert size = 138 >>>>>>> Mapping quality mean mapping quality = 24.8682 >>>>>>> ACTG content number of A's = 2,481,109,293 bp (40.94%) number of C's = 540,568,632 bp (8.92%) number of T's = 2,506,167,479 bp (41.36%) number of G's = 532,181,022 bp (8.78%) number of N's = 44,945 bp (0%) GC percentage = 17.7% >>>>>>> Mismatches and indels general error rate = 0.1949 number of mismatches = 1,151,648,535 number of insertions = 12,644,440 mapped reads with insertion percentage = 16.54% number of deletions = 11,147,131 mapped reads with deletion percentage = 15.93% homopolymer indels = 49.06% >>>>>>> Coverage mean coverageData = 10.7921X std coverageData = 12.0648X paired-end adapted mean coverage = 7.6822X There is a 83.73% of reference with a coverageData >= 1X There is a 78.26% of reference with a coverageData >= 2X There is a 72.78% of reference with a coverageData >= 3X There is a 68.26% of reference with a coverageData >= 4X There is a 63.74% of reference with a coverageData >= 5X There is a 59.52% of reference with a coverageData >= 6X There is a 55.38% of reference with a coverageData >= 7X There is a 51.45% of reference with a coverageData >= 8X There is a 47.64% of reference with a coverageData >= 9X There is a 44.01% of reference with a coverageData >= 10X There is a 40.54% of reference with a coverageData >= 11X There is a 37.26% of reference with a coverageData >= 12X There is a 34.16% of reference with a coverageData >= 13X There is a 31.25% of reference with a coverageData >= 14X There is a 28.52% of reference with a coverageData >= 15X There is a 25.97% of reference with a coverageData >= 16X There is a 23.59% of reference with a coverageData >= 17X There is a 21.39% of reference with a coverageData >= 18X There is a 19.36% of reference with a coverageData >= 19X There is a 17.48% of reference with a coverageData >= 20X There is a 15.76% of reference with a coverageData >= 21X There is a 14.19% of reference with a coverageData >= 22X There is a 12.76% of reference with a coverageData >= 23X There is a 11.45% of reference with a coverageData >= 24X There is a 10.27% of reference with a coverageData >= 25X There is a 9.21% of reference with a coverageData >= 26X There is a 8.24% of reference with a coverageData >= 27X There is a 7.38% of reference with a coverageData >= 28X There is a 6.6% of reference with a coverageData >= 29X There is a 5.91% of reference with a coverageData >= 30X There is a 5.29% of reference with a coverageData >= 31X There is a 4.74% of reference with a coverageData >= 32X There is a 4.25% of reference with a coverageData >= 33X There is a 3.81% of reference with a coverageData >= 34X There is a 3.43% of reference with a coverageData >= 35X There is a 3.09% of reference with a coverageData >= 36X There is a 2.78% of reference with a coverageData >= 37X There is a 2.52% of reference with a coverageData >= 38X There is a 2.28% of reference with a coverageData >= 39X There is a 2.07% of reference with a coverageData >= 40X There is a 1.89% of reference with a coverageData >= 41X There is a 1.72% of reference with a coverageData >= 42X There is a 1.58% of reference with a coverageData >= 43X There is a 1.45% of reference with a coverageData >= 44X There is a 1.33% of reference with a coverageData >= 45X There is a 1.23% of reference with a coverageData >= 46X There is a 1.14% of reference with a coverageData >= 47X There is a 1.06% of reference with a coverageData >= 48X There is a 0.98% of reference with a coverageData >= 49X There is a 0.92% of reference with a coverageData >= 50X There is a 0.86% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 606235565 7.969339652746209 13.014091868344797 NC_088854.1 61469542 756754745 12.311052276914639 11.824713333583171 NC_088855.1 61039741 753340458 12.341802990284641 11.671968037789659 NC_088856.1 57946171 562490614 9.707123081523367 12.337574423416852 NC_088857.1 57274926 682479709 11.91585492402033 11.656454528440086 NC_088858.1 56905015 705923114 12.40528825095644 11.179412934446436 NC_088859.1 53672946 691487157 12.883346425590277 11.899858006876528 NC_088860.1 51133819 559703146 10.945850651209916 12.072121727043408 NC_088861.1 50364239 409383422 8.128454437681468 11.157530647363007 NC_088862.1 37310742 355083329 9.516919524141331 11.926637709338022 NW_027062568.1 15579 135580 8.702740869118685 7.6981121472938945 NW_027062569.1 16498 104426 6.329615710995272 12.91802878368306 NW_027062570.1 4000 241623 60.40575 53.44102525857359 NW_027062571.1 36893 14089 0.3818881630661643 2.1416379358327213 NW_027062572.1 51000 40210 0.7884313725490196 1.8267499097038011 NW_027062573.1 2000 129468 64.734 49.789753263096216 NW_027062574.1 37061 2705 0.07298777690834031 0.6198252210214104 NW_027062575.1 49428 321600 6.506433600388444 12.89785603029024 NW_027062576.1 49232 235851 4.7906036724081895 14.483652483761182 NW_027062577.1 17087 140814 8.241001931292796 6.290387413297696 NW_027062578.1 34507 599738 17.38018373083722 9.981869351757155 NW_027062579.1 64000 454335 7.098984375 9.529686212455337 NW_027062580.1 24229 214684 8.860621569193942 8.786214549740913 NW_027062581.1 5000 16300 3.26 6.2991275586385775 NW_027062582.1 18808 292666 15.560718843045512 13.538701808765726 NW_027062583.1 1000 0 0.0 0.0 NW_027062584.1 74000 12447 0.1682027027027027 0.9470407287397369 NW_027062585.1 39334 321833 8.182056236334978 7.552129414403326 NW_027062586.1 258015 451111 1.7483905974458849 5.556028066773529