BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_26psu_2_S14.sorted.bam outfile = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_26psu_2_S14.sorted_stats/genome_results.txt >>>>>>> Reference number of bases = 2,240,221,656 bp number of contigs = 30 >>>>>>> Globals number of windows = 429 number of reads = 34,378,588 number of mapped reads = 34,378,588 (100%) number of mapped paired reads (first in pair) = 17,189,294 number of mapped paired reads (second in pair) = 17,189,294 number of mapped paired reads (both in pair) = 34,378,588 number of mapped paired reads (singletons) = 0 number of mapped bases = 3,784,331,284 bp number of sequenced bases = 3,774,038,622 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,110,088 duplication rate = 26.78% >>>>>>> Insert size mean insert size = 130.499 std insert size = 60.6231 median insert size = 120 >>>>>>> Mapping quality mean mapping quality = 23.6838 >>>>>>> ACTG content number of A's = 1,376,705,293 bp (36.48%) number of C's = 512,268,443 bp (13.57%) number of T's = 1,375,040,641 bp (36.43%) number of G's = 510,024,245 bp (13.51%) number of N's = 24,671 bp (0%) GC percentage = 27.09% >>>>>>> Mismatches and indels general error rate = 0.2085 number of mismatches = 760,662,059 number of insertions = 8,841,225 mapped reads with insertion percentage = 18.24% number of deletions = 6,195,636 mapped reads with deletion percentage = 15.38% homopolymer indels = 45.85% >>>>>>> Coverage mean coverageData = 1.6893X std coverageData = 11.4299X There is a 38.54% of reference with a coverageData >= 1X There is a 31.22% of reference with a coverageData >= 2X There is a 17.64% of reference with a coverageData >= 3X There is a 14.88% of reference with a coverageData >= 4X There is a 9.35% of reference with a coverageData >= 5X There is a 8.07% of reference with a coverageData >= 6X There is a 5.55% of reference with a coverageData >= 7X There is a 4.9% of reference with a coverageData >= 8X There is a 3.64% of reference with a coverageData >= 9X There is a 3.28% of reference with a coverageData >= 10X There is a 2.58% of reference with a coverageData >= 11X There is a 2.35% of reference with a coverageData >= 12X There is a 1.92% of reference with a coverageData >= 13X There is a 1.77% of reference with a coverageData >= 14X There is a 1.48% of reference with a coverageData >= 15X There is a 1.38% of reference with a coverageData >= 16X There is a 1.17% of reference with a coverageData >= 17X There is a 1.09% of reference with a coverageData >= 18X There is a 0.94% of reference with a coverageData >= 19X There is a 0.88% of reference with a coverageData >= 20X There is a 0.76% of reference with a coverageData >= 21X There is a 0.71% of reference with a coverageData >= 22X There is a 0.62% of reference with a coverageData >= 23X There is a 0.59% of reference with a coverageData >= 24X There is a 0.52% of reference with a coverageData >= 25X There is a 0.49% of reference with a coverageData >= 26X There is a 0.43% of reference with a coverageData >= 27X There is a 0.4% of reference with a coverageData >= 28X There is a 0.36% of reference with a coverageData >= 29X There is a 0.34% of reference with a coverageData >= 30X There is a 0.3% of reference with a coverageData >= 31X There is a 0.29% of reference with a coverageData >= 32X There is a 0.26% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.09% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_027300.1 159038749 278370823 1.7503333291435788 9.622797041611609 NC_027301.1 72943711 118756660 1.6280589288910732 6.672025322644979 NC_027302.1 92503428 151406554 1.6367669531122673 5.645437432024135 NC_027303.1 82398023 140320573 1.7029604338929345 7.405261151877041 NC_027304.1 80503876 132095137 1.6408543732726608 8.809053028868583 NC_027305.1 87043187 141043011 1.6203796742874317 12.05360751959588 NC_027306.1 58785265 98039709 1.6677599224907806 8.414940380588842 NC_027307.1 26434011 44628097 1.6882832121088245 12.29576125583028 NC_027308.1 141712163 237347223 1.6748542819150958 7.043229810185689 NC_027309.1 116138521 204982243 1.764980656159725 24.870869107442942 NC_027310.1 93888508 155593237 1.657212797544935 7.74144413519541 NC_027311.1 91880962 157960219 1.7191833385462376 11.01867873564802 NC_027312.1 107758822 185769951 1.723941924680654 7.136129418158942 NC_027313.1 93901823 159037634 1.6936586417496922 8.225606417169715 NC_027314.1 103963436 172322444 1.6575293259834158 5.6502533617426955 NC_027315.1 87796322 152497340 1.736944515739509 9.464063561977616 NC_027316.1 57682537 96057646 1.665281227141587 8.660918604596208 NC_027317.1 70695409 124333569 1.7587219701918693 9.170249330820717 NC_027318.1 82978132 140038697 1.6876578638815345 19.574262557412194 NC_027319.1 86795997 146479691 1.687631873161155 8.703031141647669 NC_027320.1 58021487 93567303 1.6126319375441032 5.479784001310402 NC_027321.1 63420196 113241888 1.7855808581859318 20.51301274492682 NC_027322.1 49854004 84227715 1.6894874682482874 7.48276475933259 NC_027323.1 48650976 76966425 1.5820119415487164 6.564150618334956 NC_027324.1 51481326 85546723 1.66170395455626 6.392528306547504 NC_027325.1 47900953 77193630 1.6115259752765252 8.57965287748269 NC_027326.1 43943985 73631909 1.6755856120012784 7.20582559228274 NC_027327.1 39600944 66812733 1.6871500083432354 12.500325518012462 NC_027328.1 42488238 65765394 1.5478494071700502 9.943664951733105 NC_001960.1 16665 10297106 617.8881488148814 946.8495188328193