BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_23.deduplicated.sorted.bam outfile = zr3644_23/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 45,049,882 number of mapped reads = 45,049,882 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 22,524,941 number of mapped paired reads (second in pair) = 22,524,941 number of mapped paired reads (both in pair) = 45,049,882 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 19,256,117 number of mapped bases = 4,726,120,546 bp number of sequenced bases = 4,705,418,109 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,167,940 duplication rate = 14.49% >>>>>>> Insert size mean insert size = 157.9854 std insert size = 69.3956 median insert size = 136 >>>>>>> Mapping quality mean mapping quality = 24.7498 >>>>>>> ACTG content number of A's = 1,927,607,288 bp (40.97%) number of C's = 418,380,790 bp (8.89%) number of T's = 1,947,315,432 bp (41.38%) number of G's = 412,078,644 bp (8.76%) number of N's = 35,955 bp (0%) GC percentage = 17.65% >>>>>>> Mismatches and indels general error rate = 0.1949 number of mismatches = 894,237,969 number of insertions = 9,852,939 mapped reads with insertion percentage = 16.59% number of deletions = 8,710,703 mapped reads with deletion percentage = 16.02% homopolymer indels = 49.05% >>>>>>> Coverage mean coverageData = 8.3799X std coverageData = 9.418X paired-end adapted mean coverage = 5.931X There is a 81.89% of reference with a coverageData >= 1X There is a 75.6% of reference with a coverageData >= 2X There is a 69.04% of reference with a coverageData >= 3X There is a 63.55% of reference with a coverageData >= 4X There is a 58.06% of reference with a coverageData >= 5X There is a 52.98% of reference with a coverageData >= 6X There is a 48.05% of reference with a coverageData >= 7X There is a 43.43% of reference with a coverageData >= 8X There is a 39.06% of reference with a coverageData >= 9X There is a 34.99% of reference with a coverageData >= 10X There is a 31.21% of reference with a coverageData >= 11X There is a 27.74% of reference with a coverageData >= 12X There is a 24.56% of reference with a coverageData >= 13X There is a 21.67% of reference with a coverageData >= 14X There is a 19.06% of reference with a coverageData >= 15X There is a 16.71% of reference with a coverageData >= 16X There is a 14.62% of reference with a coverageData >= 17X There is a 12.76% of reference with a coverageData >= 18X There is a 11.11% of reference with a coverageData >= 19X There is a 9.66% of reference with a coverageData >= 20X There is a 8.4% of reference with a coverageData >= 21X There is a 7.29% of reference with a coverageData >= 22X There is a 6.33% of reference with a coverageData >= 23X There is a 5.5% of reference with a coverageData >= 24X There is a 4.78% of reference with a coverageData >= 25X There is a 4.17% of reference with a coverageData >= 26X There is a 3.64% of reference with a coverageData >= 27X There is a 3.19% of reference with a coverageData >= 28X There is a 2.8% of reference with a coverageData >= 29X There is a 2.47% of reference with a coverageData >= 30X There is a 2.19% of reference with a coverageData >= 31X There is a 1.95% of reference with a coverageData >= 32X There is a 1.74% of reference with a coverageData >= 33X There is a 1.56% of reference with a coverageData >= 34X There is a 1.41% of reference with a coverageData >= 35X There is a 1.28% of reference with a coverageData >= 36X There is a 1.16% of reference with a coverageData >= 37X There is a 1.06% of reference with a coverageData >= 38X There is a 0.97% of reference with a coverageData >= 39X There is a 0.89% of reference with a coverageData >= 40X There is a 0.82% of reference with a coverageData >= 41X There is a 0.76% of reference with a coverageData >= 42X There is a 0.71% of reference with a coverageData >= 43X There is a 0.66% of reference with a coverageData >= 44X There is a 0.61% of reference with a coverageData >= 45X There is a 0.57% of reference with a coverageData >= 46X There is a 0.54% of reference with a coverageData >= 47X There is a 0.5% of reference with a coverageData >= 48X There is a 0.47% of reference with a coverageData >= 49X There is a 0.44% of reference with a coverageData >= 50X There is a 0.42% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 492818336 6.478400366836288 10.747364665903898 NC_088854.1 61469542 582135698 9.470311296609303 8.950770152266037 NC_088855.1 61039741 580120476 9.503979972654209 8.81559485056826 NC_088856.1 57946171 439281213 7.58084969928384 9.746433694415591 NC_088857.1 57274926 525441325 9.174020146267845 9.04402461678631 NC_088858.1 56905015 542946236 9.541272170827122 8.833999105459608 NC_088859.1 53672946 530126753 9.876982586348065 9.232297678116225 NC_088860.1 51133819 433952472 8.486603983168164 9.331613800234027 NC_088861.1 50364239 320230802 6.358297243407172 8.666694464952796 NC_088862.1 37310742 275923420 7.395280962249424 9.144096933811573 NW_027062568.1 15579 102562 6.583349380576417 5.932557987906326 NW_027062569.1 16498 183119 11.099466602012365 14.322861421608936 NW_027062570.1 4000 201229 50.30725 44.12922557033491 NW_027062571.1 36893 8750 0.2371723633209552 1.2347296808387944 NW_027062572.1 51000 17456 0.34227450980392155 0.8088538071575888 NW_027062573.1 2000 107438 53.719 44.775222902851084 NW_027062574.1 37061 4883 0.13175575402714443 0.6544267916205422 NW_027062575.1 49428 249397 5.045662377599741 10.014598726368751 NW_027062576.1 49232 144054 2.92602372440689 6.835083090983504 NW_027062577.1 17087 108741 6.363960905951894 5.612617104108168 NW_027062578.1 34507 449628 13.030051873532907 8.134455299052295 NW_027062579.1 64000 497608 7.775125 8.998135167260005 NW_027062580.1 24229 159215 6.5712575838870775 7.367643392934518 NW_027062581.1 5000 15165 3.033 6.191350983428415 NW_027062582.1 18808 38367 2.039929817099107 3.9234718977035214 NW_027062583.1 1000 0 0.0 0.0 NW_027062584.1 74000 8685 0.11736486486486486 0.7520133294447162 NW_027062585.1 39334 191029 4.856587176488534 4.889968338129676 NW_027062586.1 258015 656489 2.544383078503188 4.8616069492721135