BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_22.deduplicated.sorted.bam outfile = zr3644_22/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 53,155,204 number of mapped reads = 53,155,204 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 26,577,602 number of mapped paired reads (second in pair) = 26,577,602 number of mapped paired reads (both in pair) = 53,155,204 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 22,363,317 number of mapped bases = 5,603,163,696 bp number of sequenced bases = 5,578,695,971 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,749,365 duplication rate = 16.56% >>>>>>> Insert size mean insert size = 161.4634 std insert size = 71.6312 median insert size = 139 >>>>>>> Mapping quality mean mapping quality = 24.8469 >>>>>>> ACTG content number of A's = 2,283,514,013 bp (40.93%) number of C's = 498,027,521 bp (8.93%) number of T's = 2,306,528,889 bp (41.35%) number of G's = 490,583,448 bp (8.79%) number of N's = 42,100 bp (0%) GC percentage = 17.72% >>>>>>> Mismatches and indels general error rate = 0.195 number of mismatches = 1,061,106,867 number of insertions = 11,620,550 mapped reads with insertion percentage = 16.57% number of deletions = 10,264,765 mapped reads with deletion percentage = 15.98% homopolymer indels = 49.05% >>>>>>> Coverage mean coverageData = 9.9349X std coverageData = 11.2036X paired-end adapted mean coverage = 7.1057X There is a 83.09% of reference with a coverageData >= 1X There is a 77.33% of reference with a coverageData >= 2X There is a 71.53% of reference with a coverageData >= 3X There is a 66.69% of reference with a coverageData >= 4X There is a 61.86% of reference with a coverageData >= 5X There is a 57.36% of reference with a coverageData >= 6X There is a 52.98% of reference with a coverageData >= 7X There is a 48.83% of reference with a coverageData >= 8X There is a 44.84% of reference with a coverageData >= 9X There is a 41.08% of reference with a coverageData >= 10X There is a 37.52% of reference with a coverageData >= 11X There is a 34.16% of reference with a coverageData >= 12X There is a 31.01% of reference with a coverageData >= 13X There is a 28.08% of reference with a coverageData >= 14X There is a 25.36% of reference with a coverageData >= 15X There is a 22.85% of reference with a coverageData >= 16X There is a 20.53% of reference with a coverageData >= 17X There is a 18.41% of reference with a coverageData >= 18X There is a 16.48% of reference with a coverageData >= 19X There is a 14.72% of reference with a coverageData >= 20X There is a 13.12% of reference with a coverageData >= 21X There is a 11.68% of reference with a coverageData >= 22X There is a 10.38% of reference with a coverageData >= 23X There is a 9.22% of reference with a coverageData >= 24X There is a 8.18% of reference with a coverageData >= 25X There is a 7.26% of reference with a coverageData >= 26X There is a 6.44% of reference with a coverageData >= 27X There is a 5.71% of reference with a coverageData >= 28X There is a 5.07% of reference with a coverageData >= 29X There is a 4.51% of reference with a coverageData >= 30X There is a 4.01% of reference with a coverageData >= 31X There is a 3.58% of reference with a coverageData >= 32X There is a 3.2% of reference with a coverageData >= 33X There is a 2.86% of reference with a coverageData >= 34X There is a 2.57% of reference with a coverageData >= 35X There is a 2.31% of reference with a coverageData >= 36X There is a 2.09% of reference with a coverageData >= 37X There is a 1.89% of reference with a coverageData >= 38X There is a 1.72% of reference with a coverageData >= 39X There is a 1.57% of reference with a coverageData >= 40X There is a 1.44% of reference with a coverageData >= 41X There is a 1.32% of reference with a coverageData >= 42X There is a 1.21% of reference with a coverageData >= 43X There is a 1.12% of reference with a coverageData >= 44X There is a 1.04% of reference with a coverageData >= 45X There is a 0.96% of reference with a coverageData >= 46X There is a 0.9% of reference with a coverageData >= 47X There is a 0.84% of reference with a coverageData >= 48X There is a 0.78% of reference with a coverageData >= 49X There is a 0.73% of reference with a coverageData >= 50X There is a 0.69% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 574441191 7.551383036406086 12.724317396626617 NC_088854.1 61469542 689208197 11.212190209583797 10.78420919990156 NC_088855.1 61039741 688238459 11.275251954296465 10.578733211461849 NC_088856.1 57946171 521249596 8.995410516425666 11.37799594320332 NC_088857.1 57274926 624617386 10.905599179648002 10.731004367168335 NC_088858.1 56905015 644336467 11.32301725955085 10.258769401483294 NC_088859.1 53672946 630360693 11.744477245575453 11.020246851824513 NC_088860.1 51133819 520455375 10.178300490327155 11.227799390807316 NC_088861.1 50364239 379960649 7.544254743926539 10.095856936318777 NC_088862.1 37310742 327040853 8.765326966695007 11.424018267312409 NW_027062568.1 15579 118804 7.625906669234226 6.987942035945196 NW_027062569.1 16498 110065 6.671414716935386 13.769727688695378 NW_027062570.1 4000 51214 12.8035 13.556369360931415 NW_027062571.1 36893 9122 0.24725557693871467 1.0014857743069585 NW_027062572.1 51000 38334 0.7516470588235294 1.878510015955767 NW_027062573.1 2000 51738 25.869 14.592077199631314 NW_027062574.1 37061 3712 0.1001591969995413 0.5721520916123323 NW_027062575.1 49428 308737 6.246196487820669 12.641115649049143 NW_027062576.1 49232 171363 3.4807239194020148 7.647405809771696 NW_027062577.1 17087 133373 7.805524667876163 5.811160815164675 NW_027062578.1 34507 550936 15.965919958269337 8.576808179812245 NW_027062579.1 64000 394256 6.16025 8.087652638629146 NW_027062580.1 24229 163217 6.736431548970242 7.504501016386649 NW_027062581.1 5000 12720 2.544 6.949891279725173 NW_027062582.1 18808 249079 13.24324755423224 11.202200142953439 NW_027062583.1 1000 0 0.0 0.0 NW_027062584.1 74000 11078 0.1497027027027027 0.9049314257543221 NW_027062585.1 39334 240219 6.107159200691513 6.534780719749343 NW_027062586.1 258015 636863 2.4683177334651085 5.41095533817514