BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18.sorted.bam outfile = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18.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 = 34,603,430 number of mapped reads = 34,603,430 (100%) number of mapped paired reads (first in pair) = 17,301,715 number of mapped paired reads (second in pair) = 17,301,715 number of mapped paired reads (both in pair) = 34,603,430 number of mapped paired reads (singletons) = 0 number of mapped bases = 3,143,580,489 bp number of sequenced bases = 3,135,603,790 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,470,956 duplication rate = 28.52% >>>>>>> Insert size mean insert size = 100.6303 std insert size = 44.5324 median insert size = 92 >>>>>>> Mapping quality mean mapping quality = 23.5659 >>>>>>> ACTG content number of A's = 1,109,818,749 bp (35.39%) number of C's = 458,267,483 bp (14.61%) number of T's = 1,109,074,766 bp (35.37%) number of G's = 458,442,792 bp (14.62%) number of N's = 18,310 bp (0%) GC percentage = 29.24% >>>>>>> Mismatches and indels general error rate = 0.2052 number of mismatches = 624,416,330 number of insertions = 6,851,107 mapped reads with insertion percentage = 14.7% number of deletions = 4,872,532 mapped reads with deletion percentage = 12.25% homopolymer indels = 43.13% >>>>>>> Coverage mean coverageData = 1.4032X std coverageData = 12.8932X There is a 28.29% of reference with a coverageData >= 1X There is a 24.9% of reference with a coverageData >= 2X There is a 12.79% of reference with a coverageData >= 3X There is a 11.6% of reference with a coverageData >= 4X There is a 7.12% of reference with a coverageData >= 5X There is a 6.54% of reference with a coverageData >= 6X There is a 4.57% of reference with a coverageData >= 7X There is a 4.25% of reference with a coverageData >= 8X There is a 3.24% of reference with a coverageData >= 9X There is a 3.03% of reference with a coverageData >= 10X There is a 2.45% of reference with a coverageData >= 11X There is a 2.3% of reference with a coverageData >= 12X There is a 1.92% of reference with a coverageData >= 13X There is a 1.81% of reference with a coverageData >= 14X There is a 1.54% of reference with a coverageData >= 15X There is a 1.45% of reference with a coverageData >= 16X There is a 1.25% of reference with a coverageData >= 17X There is a 1.19% of reference with a coverageData >= 18X There is a 1.03% of reference with a coverageData >= 19X There is a 0.98% of reference with a coverageData >= 20X There is a 0.86% of reference with a coverageData >= 21X There is a 0.81% of reference with a coverageData >= 22X There is a 0.72% of reference with a coverageData >= 23X There is a 0.68% of reference with a coverageData >= 24X There is a 0.6% of reference with a coverageData >= 25X There is a 0.57% of reference with a coverageData >= 26X There is a 0.51% of reference with a coverageData >= 27X There is a 0.49% of reference with a coverageData >= 28X There is a 0.44% of reference with a coverageData >= 29X There is a 0.41% of reference with a coverageData >= 30X There is a 0.37% of reference with a coverageData >= 31X There is a 0.36% of reference with a coverageData >= 32X There is a 0.32% of reference with a coverageData >= 33X There is a 0.31% of reference with a coverageData >= 34X There is a 0.28% of reference with a coverageData >= 35X There is a 0.27% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.12% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_027300.1 159038749 230096766 1.4467968809286849 8.127124036515124 NC_027301.1 72943711 96991323 1.3296735478676154 6.991419284341901 NC_027302.1 92503428 124046747 1.3409962169185774 5.481226352243411 NC_027303.1 82398023 116256271 1.4109109268313391 9.807901787407777 NC_027304.1 80503876 109307513 1.3577919279315198 8.304629214645828 NC_027305.1 87043187 115013011 1.3213327195843598 10.450580605328204 NC_027306.1 58785265 82261828 1.3993613535636864 9.016860301638866 NC_027307.1 26434011 36865301 1.3946162389052497 12.595617467822043 NC_027308.1 141712163 197116301 1.3909624751123162 7.606310605743522 NC_027309.1 116138521 171457762 1.476321211288716 19.94196134959535 NC_027310.1 93888508 127674516 1.3598524326321173 6.887356153323235 NC_027311.1 91880962 129233937 1.4065366120132698 9.477255817692422 NC_027312.1 107758822 153734108 1.4266498570298032 6.8814238911607575 NC_027313.1 93901823 132450845 1.4105247456164935 12.479849176919524 NC_027314.1 103963436 142677306 1.3723796700986297 6.1227324889311205 NC_027315.1 87796322 125720396 1.4319551563902644 10.764208722447044 NC_027316.1 57682537 77712902 1.3472518034357608 9.140798238986397 NC_027317.1 70695409 102620669 1.451588871916704 10.88150402894866 NC_027318.1 82978132 120775022 1.4555042285116757 35.25810609235685 NC_027319.1 86795997 121240674 1.3968463776042574 6.803689678566901 NC_027320.1 58021487 78086497 1.3458203337670405 5.194999696611421 NC_027321.1 63420196 96056816 1.5146092579089474 26.883290503970702 NC_027322.1 49854004 70952225 1.423200130525123 7.95454448302172 NC_027323.1 48650976 63403380 1.3032293535077282 6.311632382644978 NC_027324.1 51481326 71935108 1.3973048790545917 7.457804789089993 NC_027325.1 47900953 61724586 1.2885878491812053 7.474795722631757 NC_027326.1 43943985 62661431 1.4259387490688429 9.354553656392586 NC_027327.1 39600944 57901130 1.4621148930187118 13.16860068754122 NC_027328.1 42488238 54999038 1.2944532555103838 9.084073908797128 NC_001960.1 16665 12607080 756.5004500450045 1112.538720480479