BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21.sorted.bam outfile = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21.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 = 25,716,104 number of mapped reads = 25,716,104 (100%) number of mapped paired reads (first in pair) = 12,858,052 number of mapped paired reads (second in pair) = 12,858,052 number of mapped paired reads (both in pair) = 25,716,104 number of mapped paired reads (singletons) = 0 number of mapped bases = 2,499,586,182 bp number of sequenced bases = 2,492,058,274 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,218,919 duplication rate = 22.29% >>>>>>> Insert size mean insert size = 107.1819 std insert size = 43.0236 median insert size = 100 >>>>>>> Mapping quality mean mapping quality = 21.0849 >>>>>>> ACTG content number of A's = 885,166,319 bp (35.52%) number of C's = 363,228,368 bp (14.58%) number of T's = 883,372,273 bp (35.45%) number of G's = 360,291,314 bp (14.46%) number of N's = 14,647 bp (0%) GC percentage = 29.03% >>>>>>> Mismatches and indels general error rate = 0.2166 number of mismatches = 518,329,887 number of insertions = 7,546,269 mapped reads with insertion percentage = 21.56% number of deletions = 4,686,411 mapped reads with deletion percentage = 15.69% homopolymer indels = 41.11% >>>>>>> Coverage mean coverageData = 1.1158X std coverageData = 10.7513X There is a 24.51% of reference with a coverageData >= 1X There is a 21.41% of reference with a coverageData >= 2X There is a 10.23% of reference with a coverageData >= 3X There is a 9.21% of reference with a coverageData >= 4X There is a 5.6% of reference with a coverageData >= 5X There is a 5.12% of reference with a coverageData >= 6X There is a 3.63% of reference with a coverageData >= 7X There is a 3.36% of reference with a coverageData >= 8X There is a 2.6% of reference with a coverageData >= 9X There is a 2.42% of reference with a coverageData >= 10X There is a 1.95% of reference with a coverageData >= 11X There is a 1.82% of reference with a coverageData >= 12X There is a 1.51% of reference with a coverageData >= 13X There is a 1.41% of reference with a coverageData >= 14X There is a 1.18% of reference with a coverageData >= 15X There is a 1.11% of reference with a coverageData >= 16X There is a 0.94% of reference with a coverageData >= 17X There is a 0.88% of reference with a coverageData >= 18X There is a 0.75% of reference with a coverageData >= 19X There is a 0.71% of reference with a coverageData >= 20X There is a 0.6% of reference with a coverageData >= 21X There is a 0.57% of reference with a coverageData >= 22X There is a 0.49% of reference with a coverageData >= 23X There is a 0.46% of reference with a coverageData >= 24X There is a 0.4% of reference with a coverageData >= 25X There is a 0.38% of reference with a coverageData >= 26X There is a 0.33% of reference with a coverageData >= 27X There is a 0.31% of reference with a coverageData >= 28X There is a 0.27% of reference with a coverageData >= 29X There is a 0.25% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.15% of reference with a coverageData >= 36X There is a 0.13% of reference with a coverageData >= 37X There is a 0.13% of reference with a coverageData >= 38X There is a 0.11% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.07% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_027300.1 159038749 184107560 1.1576270635780719 5.809936954848573 NC_027301.1 72943711 75988043 1.0417353594746503 4.5313990909752375 NC_027302.1 92503428 98811669 1.0681946727422902 4.07569800292746 NC_027303.1 82398023 94013586 1.1409689526167393 9.055464925695585 NC_027304.1 80503876 85847933 1.0663826049816534 6.511272304404011 NC_027305.1 87043187 90096321 1.035076082404933 7.443073407657225 NC_027306.1 58785265 63837548 1.085944717609081 5.828056255906642 NC_027307.1 26434011 28988500 1.096636450669556 9.697662825068678 NC_027308.1 141712163 155336762 1.0961427636948848 5.629969188305775 NC_027309.1 116138521 136149232 1.1723003774088014 13.5800267979564 NC_027310.1 93888508 101365686 1.0796389053280089 5.324680864573696 NC_027311.1 91880962 104142033 1.1334451744203549 8.99415707347791 NC_027312.1 107758822 123676598 1.1477166853215972 5.824858809676351 NC_027313.1 93901823 104895661 1.1170780039062713 8.05512875807862 NC_027314.1 103963436 113122739 1.0881011955010798 4.516343697852411 NC_027315.1 87796322 99646566 1.1349742646394687 6.0172516938384595 NC_027316.1 57682537 59918835 1.0387690645437457 5.112779064865904 NC_027317.1 70695409 80854496 1.1437022169289663 8.196791465863777 NC_027318.1 82978132 95964223 1.156500160789351 29.92788653575798 NC_027319.1 86795997 96466545 1.1114169815919046 5.592829370514317 NC_027320.1 58021487 62702866 1.0806835405648945 4.010748176659564 NC_027321.1 63420196 76597573 1.2077788753601455 19.897036700177804 NC_027322.1 49854004 57121376 1.1457730857485389 5.710794219435207 NC_027323.1 48650976 50921091 1.046661242726148 4.320483445148233 NC_027324.1 51481326 57192841 1.1109434321874305 5.58423265381447 NC_027325.1 47900953 47959267 1.0012173870528214 5.306794435730154 NC_027326.1 43943985 49023628 1.1155935903400658 6.1873621017688905 NC_027327.1 39600944 45449119 1.1476776664717891 7.972852117748071 NC_027328.1 42488238 43364173 1.0206159408163737 6.623089305143402 NC_001960.1 16665 16023712 961.5188718871888 1622.0132957392516