BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_9.deduplicated.sorted.bam outfile = zr3644_9/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 52,631,226 number of mapped reads = 52,631,226 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 26,315,613 number of mapped paired reads (second in pair) = 26,315,613 number of mapped paired reads (both in pair) = 52,631,226 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 23,293,629 number of mapped bases = 5,428,878,929 bp number of sequenced bases = 5,405,274,113 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,356,431 duplication rate = 16.08% >>>>>>> Insert size mean insert size = 149.3858 std insert size = 65.2135 median insert size = 128 >>>>>>> Mapping quality mean mapping quality = 24.636 >>>>>>> ACTG content number of A's = 2,210,778,570 bp (40.9%) number of C's = 484,151,180 bp (8.96%) number of T's = 2,233,878,763 bp (41.33%) number of G's = 476,424,516 bp (8.81%) number of N's = 41,084 bp (0%) GC percentage = 17.77% >>>>>>> Mismatches and indels general error rate = 0.1957 number of mismatches = 1,031,935,592 number of insertions = 11,404,149 mapped reads with insertion percentage = 16.42% number of deletions = 10,037,739 mapped reads with deletion percentage = 15.82% homopolymer indels = 49.09% >>>>>>> Coverage mean coverageData = 9.6259X std coverageData = 10.8821X paired-end adapted mean coverage = 6.6285X There is a 82.79% of reference with a coverageData >= 1X There is a 77.25% of reference with a coverageData >= 2X There is a 71.35% of reference with a coverageData >= 3X There is a 66.52% of reference with a coverageData >= 4X There is a 61.54% of reference with a coverageData >= 5X There is a 56.92% of reference with a coverageData >= 6X There is a 52.35% of reference with a coverageData >= 7X There is a 48.03% of reference with a coverageData >= 8X There is a 43.87% of reference with a coverageData >= 9X There is a 39.95% of reference with a coverageData >= 10X There is a 36.24% of reference with a coverageData >= 11X There is a 32.8% of reference with a coverageData >= 12X There is a 29.58% of reference with a coverageData >= 13X There is a 26.61% of reference with a coverageData >= 14X There is a 23.88% of reference with a coverageData >= 15X There is a 21.38% of reference with a coverageData >= 16X There is a 19.1% of reference with a coverageData >= 17X There is a 17.03% of reference with a coverageData >= 18X There is a 15.16% of reference with a coverageData >= 19X There is a 13.47% of reference with a coverageData >= 20X There is a 11.96% of reference with a coverageData >= 21X There is a 10.61% of reference with a coverageData >= 22X There is a 9.4% of reference with a coverageData >= 23X There is a 8.33% of reference with a coverageData >= 24X There is a 7.37% of reference with a coverageData >= 25X There is a 6.53% of reference with a coverageData >= 26X There is a 5.78% of reference with a coverageData >= 27X There is a 5.13% of reference with a coverageData >= 28X There is a 4.55% of reference with a coverageData >= 29X There is a 4.05% of reference with a coverageData >= 30X There is a 3.61% of reference with a coverageData >= 31X There is a 3.22% of reference with a coverageData >= 32X There is a 2.88% of reference with a coverageData >= 33X There is a 2.59% of reference with a coverageData >= 34X There is a 2.33% of reference with a coverageData >= 35X There is a 2.1% of reference with a coverageData >= 36X There is a 1.9% of reference with a coverageData >= 37X There is a 1.73% of reference with a coverageData >= 38X There is a 1.58% of reference with a coverageData >= 39X There is a 1.44% of reference with a coverageData >= 40X There is a 1.32% of reference with a coverageData >= 41X There is a 1.22% of reference with a coverageData >= 42X There is a 1.13% of reference with a coverageData >= 43X There is a 1.04% of reference with a coverageData >= 44X There is a 0.97% of reference with a coverageData >= 45X There is a 0.9% of reference with a coverageData >= 46X There is a 0.84% of reference with a coverageData >= 47X There is a 0.79% of reference with a coverageData >= 48X There is a 0.74% of reference with a coverageData >= 49X There is a 0.69% of reference with a coverageData >= 50X There is a 0.65% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 555656170 7.304442372783075 12.181339774024856 NC_088854.1 61469542 666041655 10.835311819957923 10.365305947607808 NC_088855.1 61039741 666090811 10.912412144736983 10.641692252360906 NC_088856.1 57946171 505975152 8.731813392812443 10.773267536924696 NC_088857.1 57274926 603292998 10.533282888920713 10.448458732720733 NC_088858.1 56905015 622481874 10.938963358501882 10.049920889919765 NC_088859.1 53672946 611280956 11.38899578942434 11.130756690368306 NC_088860.1 51133819 503616448 9.848989530783921 10.770340680470888 NC_088861.1 50364239 371025927 7.3668526392307845 9.853182307625378 NC_088862.1 37310742 320318579 8.58515703064817 10.912482180378499 NW_027062568.1 15579 120415 7.72931510366519 6.927278478632762 NW_027062569.1 16498 106081 6.429930900715238 14.1925138961535 NW_027062570.1 4000 55743 13.93575 12.709362397952937 NW_027062571.1 36893 9594 0.26004933185157075 1.909976728551403 NW_027062572.1 51000 22271 0.4366862745098039 1.0578682936913202 NW_027062573.1 2000 43629 21.8145 11.153888010465227 NW_027062574.1 37061 446 0.012034213863630232 0.1500683618375234 NW_027062575.1 49428 389893 7.888099862426155 14.857986530542968 NW_027062576.1 49232 233402 4.740859603509913 19.479416114176313 NW_027062577.1 17087 136612 7.9950839819746005 5.92133473903683 NW_027062578.1 34507 515121 14.92801460573217 8.845014270603878 NW_027062579.1 64000 406723 6.355046875 7.7707440526997384 NW_027062580.1 24229 244103 10.074827685831028 9.707572261035715 NW_027062581.1 5000 13782 2.7564 6.325076846963996 NW_027062582.1 18808 152441 8.105114844746916 7.178941436551015 NW_027062583.1 1000 0 0.0 0.0 NW_027062584.1 74000 10533 0.14233783783783785 0.6866780793769807 NW_027062585.1 39334 241684 6.144404332129964 6.539331244794767 NW_027062586.1 258015 395886 1.53435265391547 4.898151828289053