BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/8C_32psu_4_S8.sorted.bam outfile = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/8C_32psu_4_S8.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 = 28,602,080 number of mapped reads = 28,602,080 (100%) number of mapped paired reads (first in pair) = 14,301,040 number of mapped paired reads (second in pair) = 14,301,040 number of mapped paired reads (both in pair) = 28,602,080 number of mapped paired reads (singletons) = 0 number of mapped bases = 3,206,206,788 bp number of sequenced bases = 3,196,871,300 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,303,004 duplication rate = 23.7% >>>>>>> Insert size mean insert size = 132.7155 std insert size = 59.5112 median insert size = 122 >>>>>>> Mapping quality mean mapping quality = 23.0811 >>>>>>> ACTG content number of A's = 1,181,364,185 bp (36.95%) number of C's = 418,851,610 bp (13.1%) number of T's = 1,180,272,409 bp (36.92%) number of G's = 416,383,096 bp (13.02%) number of N's = 21,659 bp (0%) GC percentage = 26.13% >>>>>>> Mismatches and indels general error rate = 0.2192 number of mismatches = 674,659,390 number of insertions = 8,706,112 mapped reads with insertion percentage = 21.51% number of deletions = 5,735,343 mapped reads with deletion percentage = 17.05% homopolymer indels = 46.9% >>>>>>> Coverage mean coverageData = 1.4312X std coverageData = 11.4631X There is a 34.57% of reference with a coverageData >= 1X There is a 27.43% of reference with a coverageData >= 2X There is a 14.63% of reference with a coverageData >= 3X There is a 12.18% of reference with a coverageData >= 4X There is a 7.49% of reference with a coverageData >= 5X There is a 6.44% of reference with a coverageData >= 6X There is a 4.47% of reference with a coverageData >= 7X There is a 3.95% of reference with a coverageData >= 8X There is a 2.99% of reference with a coverageData >= 9X There is a 2.7% of reference with a coverageData >= 10X There is a 2.16% of reference with a coverageData >= 11X There is a 1.98% of reference with a coverageData >= 12X There is a 1.63% of reference with a coverageData >= 13X There is a 1.51% of reference with a coverageData >= 14X There is a 1.27% of reference with a coverageData >= 15X There is a 1.17% of reference with a coverageData >= 16X There is a 1% of reference with a coverageData >= 17X There is a 0.93% of reference with a coverageData >= 18X There is a 0.8% of reference with a coverageData >= 19X There is a 0.74% of reference with a coverageData >= 20X There is a 0.64% of reference with a coverageData >= 21X There is a 0.6% of reference with a coverageData >= 22X There is a 0.52% of reference with a coverageData >= 23X There is a 0.49% of reference with a coverageData >= 24X There is a 0.43% of reference with a coverageData >= 25X There is a 0.4% of reference with a coverageData >= 26X There is a 0.35% of reference with a coverageData >= 27X There is a 0.33% of reference with a coverageData >= 28X There is a 0.29% of reference with a coverageData >= 29X There is a 0.28% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.13% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.1% of reference with a coverageData >= 44X There is a 0.09% of reference with a coverageData >= 45X There is a 0.09% of reference with a coverageData >= 46X There is a 0.08% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_027300.1 159038749 237397167 1.4927001657941865 10.517332042813914 NC_027301.1 72943711 98686787 1.3529170047298527 5.485398984121425 NC_027302.1 92503428 128369659 1.3877286688229544 4.765285214106765 NC_027303.1 82398023 120406885 1.461283664536466 9.038659099070975 NC_027304.1 80503876 109806937 1.3639956540726064 7.217953201305509 NC_027305.1 87043187 118006829 1.3557273471615878 11.294922751585908 NC_027306.1 58785265 81907553 1.3933347582935962 6.6817576589758385 NC_027307.1 26434011 37941910 1.4353444129231845 10.742198982453985 NC_027308.1 141712163 197871967 1.3962948755499553 6.370348140134607 NC_027309.1 116138521 174228607 1.5001793160427797 22.41257587852393 NC_027310.1 93888508 130283632 1.3876419465521808 6.199452973726301 NC_027311.1 91880962 134548936 1.4643831874550899 11.058030748053643 NC_027312.1 107758822 157632631 1.4628280828830886 6.411630394608917 NC_027313.1 93901823 133750011 1.4243601106657962 9.823289344338892 NC_027314.1 103963436 145106608 1.3957465584342557 4.586029567712167 NC_027315.1 87796322 127772873 1.45533286690529 7.01227201264716 NC_027316.1 57682537 79443062 1.3772463232676468 7.042566860352189 NC_027317.1 70695409 105510092 1.49246030955136 8.528003391941615 NC_027318.1 82978132 121307918 1.461926354283319 24.70417282538136 NC_027319.1 86795997 124779121 1.4376137761284082 6.8452062164596414 NC_027320.1 58021487 80530372 1.3879405055578806 4.973761009725305 NC_027321.1 63420196 97855077 1.542963963719065 23.710232020410807 NC_027322.1 49854004 73517243 1.474650722136581 6.78163240684813 NC_027323.1 48650976 65519509 1.346725479875265 4.697422098741103 NC_027324.1 51481326 72643740 1.4110697148709805 5.575223012527899 NC_027325.1 47900953 64582059 1.3482416310172367 6.468598704334909 NC_027326.1 43943985 62658384 1.4258694107964947 7.190221003278656 NC_027327.1 39600944 56553296 1.4280794922464475 8.113276081253263 NC_027328.1 42488238 56340485 1.3260254520321602 11.279288374598561 NC_001960.1 16665 11247438 674.9137713771377 1129.8674920686933