BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19.sorted.bam outfile = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19.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 = 34,900,622 number of mapped reads = 34,900,622 (100%) number of mapped paired reads (first in pair) = 17,450,311 number of mapped paired reads (second in pair) = 17,450,311 number of mapped paired reads (both in pair) = 34,900,622 number of mapped paired reads (singletons) = 0 number of mapped bases = 3,753,814,741 bp number of sequenced bases = 3,743,362,069 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,424,033 duplication rate = 25.74% >>>>>>> Insert size mean insert size = 124.004 std insert size = 54.5676 median insert size = 115 >>>>>>> Mapping quality mean mapping quality = 23.1111 >>>>>>> ACTG content number of A's = 1,360,794,773 bp (36.35%) number of C's = 511,864,593 bp (13.67%) number of T's = 1,360,169,007 bp (36.34%) number of G's = 510,533,696 bp (13.64%) number of N's = 23,982 bp (0%) GC percentage = 27.31% >>>>>>> Mismatches and indels general error rate = 0.2126 number of mismatches = 767,196,564 number of insertions = 9,631,319 mapped reads with insertion percentage = 19.26% number of deletions = 6,391,426 mapped reads with deletion percentage = 15.6% homopolymer indels = 45.31% >>>>>>> Coverage mean coverageData = 1.6756X std coverageData = 12.7065X There is a 34.63% of reference with a coverageData >= 1X There is a 28.37% of reference with a coverageData >= 2X There is a 15.43% of reference with a coverageData >= 3X There is a 13.24% of reference with a coverageData >= 4X There is a 8.47% of reference with a coverageData >= 5X There is a 7.49% of reference with a coverageData >= 6X There is a 5.45% of reference with a coverageData >= 7X There is a 4.94% of reference with a coverageData >= 8X There is a 3.91% of reference with a coverageData >= 9X There is a 3.6% of reference with a coverageData >= 10X There is a 3.01% of reference with a coverageData >= 11X There is a 2.8% of reference with a coverageData >= 12X There is a 2.4% of reference with a coverageData >= 13X There is a 2.24% of reference with a coverageData >= 14X There is a 1.95% of reference with a coverageData >= 15X There is a 1.84% of reference with a coverageData >= 16X There is a 1.61% of reference with a coverageData >= 17X There is a 1.52% of reference with a coverageData >= 18X There is a 1.34% of reference with a coverageData >= 19X There is a 1.27% of reference with a coverageData >= 20X There is a 1.12% of reference with a coverageData >= 21X There is a 1.06% of reference with a coverageData >= 22X There is a 0.95% of reference with a coverageData >= 23X There is a 0.9% of reference with a coverageData >= 24X There is a 0.8% of reference with a coverageData >= 25X There is a 0.76% of reference with a coverageData >= 26X There is a 0.68% of reference with a coverageData >= 27X There is a 0.65% of reference with a coverageData >= 28X There is a 0.58% of reference with a coverageData >= 29X There is a 0.55% of reference with a coverageData >= 30X There is a 0.5% of reference with a coverageData >= 31X There is a 0.47% of reference with a coverageData >= 32X There is a 0.43% of reference with a coverageData >= 33X There is a 0.41% of reference with a coverageData >= 34X There is a 0.37% of reference with a coverageData >= 35X There is a 0.35% of reference with a coverageData >= 36X There is a 0.32% of reference with a coverageData >= 37X There is a 0.31% of reference with a coverageData >= 38X There is a 0.28% of reference with a coverageData >= 39X There is a 0.27% of reference with a coverageData >= 40X There is a 0.25% of reference with a coverageData >= 41X There is a 0.24% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_027300.1 159038749 277840406 1.7469981859578134 9.119296347705333 NC_027301.1 72943711 116134203 1.5921071386126764 7.0855440608202995 NC_027302.1 92503428 150488758 1.6268452018880857 5.8965925681143 NC_027303.1 82398023 140161012 1.7010239675289296 9.512362355214128 NC_027304.1 80503876 129420116 1.6076258986585938 9.176826559940327 NC_027305.1 87043187 137887832 1.584131242804793 14.366296626647582 NC_027306.1 58785265 96417077 1.6401572230728227 8.598526859495198 NC_027307.1 26434011 43908678 1.6610675542202051 13.40766701874782 NC_027308.1 141712163 234208645 1.6527067263802897 7.634864652630373 NC_027309.1 116138521 206221960 1.7756551247970516 26.5509988029566 NC_027310.1 93888508 153726935 1.6373349441233 7.124532711560599 NC_027311.1 91880962 155487080 1.6922665655154983 10.015514351400286 NC_027312.1 107758822 185139462 1.7180909976911218 7.951022172100764 NC_027313.1 93901823 157557090 1.6778917061067067 7.954390870558556 NC_027314.1 103963436 170586098 1.6408278195037724 6.196470582500976 NC_027315.1 87796322 151919000 1.73035722384817 10.126120578786333 NC_027316.1 57682537 92661461 1.6064040491145526 9.176211885248506 NC_027317.1 70695409 122240624 1.7291168652832887 10.600890638127552 NC_027318.1 82978132 142278714 1.714653132948329 28.173904541491556 NC_027319.1 86795997 145698791 1.678634914465007 7.704600022343533 NC_027320.1 58021487 94290514 1.6250964750351882 5.933530407539675 NC_027321.1 63420196 114456303 1.8047295691107608 25.31593316853888 NC_027322.1 49854004 85734400 1.7197094139118696 9.612090491026066 NC_027323.1 48650976 75939707 1.5609081922631933 6.060179550017493 NC_027324.1 51481326 85332153 1.6575360354937245 7.613367172599183 NC_027325.1 47900953 74163454 1.5482667745670948 7.532495138504464 NC_027326.1 43943985 73230042 1.6664406289051847 8.613957349186931 NC_027327.1 39600944 66581611 1.6813137333291852 11.237352819339227 NC_027328.1 42488238 65606186 1.5441022995587625 12.733318903235158 NC_001960.1 16665 8496429 509.8367236723672 862.090319488853