BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17.sorted.bam outfile = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17.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 = 28,751,448 number of mapped reads = 28,751,448 (100%) number of mapped paired reads (first in pair) = 14,375,724 number of mapped paired reads (second in pair) = 14,375,724 number of mapped paired reads (both in pair) = 28,751,448 number of mapped paired reads (singletons) = 0 number of mapped bases = 3,206,061,298 bp number of sequenced bases = 3,197,481,015 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,871,737 duplication rate = 29.31% >>>>>>> Insert size mean insert size = 136.0432 std insert size = 66.6616 median insert size = 123 >>>>>>> Mapping quality mean mapping quality = 25.3122 >>>>>>> ACTG content number of A's = 1,196,463,142 bp (37.42%) number of C's = 404,189,548 bp (12.64%) number of T's = 1,195,164,434 bp (37.38%) number of G's = 401,663,891 bp (12.56%) number of N's = 18,397 bp (0%) GC percentage = 25.2% >>>>>>> Mismatches and indels general error rate = 0.202 number of mismatches = 627,433,268 number of insertions = 6,469,093 mapped reads with insertion percentage = 16.07% number of deletions = 5,172,131 mapped reads with deletion percentage = 15.45% homopolymer indels = 47.43% >>>>>>> Coverage mean coverageData = 1.4311X std coverageData = 11.9724X There is a 35.63% of reference with a coverageData >= 1X There is a 28.39% of reference with a coverageData >= 2X There is a 15.79% of reference with a coverageData >= 3X There is a 13.23% of reference with a coverageData >= 4X There is a 8% of reference with a coverageData >= 5X There is a 6.84% of reference with a coverageData >= 6X There is a 4.44% of reference with a coverageData >= 7X There is a 3.86% of reference with a coverageData >= 8X There is a 2.68% of reference with a coverageData >= 9X There is a 2.37% of reference with a coverageData >= 10X There is a 1.74% of reference with a coverageData >= 11X There is a 1.56% of reference with a coverageData >= 12X There is a 1.21% of reference with a coverageData >= 13X There is a 1.1% of reference with a coverageData >= 14X There is a 0.88% of reference with a coverageData >= 15X There is a 0.81% of reference with a coverageData >= 16X There is a 0.67% of reference with a coverageData >= 17X There is a 0.62% of reference with a coverageData >= 18X There is a 0.52% of reference with a coverageData >= 19X There is a 0.49% of reference with a coverageData >= 20X There is a 0.42% of reference with a coverageData >= 21X There is a 0.39% of reference with a coverageData >= 22X There is a 0.34% of reference with a coverageData >= 23X There is a 0.32% of reference with a coverageData >= 24X There is a 0.29% of reference with a coverageData >= 25X There is a 0.27% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.14% of reference with a coverageData >= 35X There is a 0.13% of reference with a coverageData >= 36X There is a 0.13% of reference with a coverageData >= 37X There is a 0.12% 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 0.1% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.09% of reference with a coverageData >= 45X There is a 0.08% 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 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_027300.1 159038749 237750512 1.494921919940404 9.278687184505843 NC_027301.1 72943711 101120495 1.3862811970177937 7.916281363351463 NC_027302.1 92503428 129305799 1.3978487262115302 5.912389822175732 NC_027303.1 82398023 118746218 1.4411294552540417 5.768137119024693 NC_027304.1 80503876 111676864 1.3872234425085321 10.352411678128496 NC_027305.1 87043187 117275337 1.3473235647954849 8.367396590250074 NC_027306.1 58785265 82082718 1.3963145016017193 8.495208950896302 NC_027307.1 26434011 38148038 1.4431422457984149 8.886021125410409 NC_027308.1 141712163 197995035 1.3971633119452138 6.208875996158087 NC_027309.1 116138521 176602101 1.52061606673982 34.64637453922053 NC_027310.1 93888508 132009951 1.4060288507300596 6.913844161662623 NC_027311.1 91880962 132405106 1.4410504974904377 7.1038433606352305 NC_027312.1 107758822 157322974 1.459954471291455 8.192366809119946 NC_027313.1 93901823 133173694 1.4182226685844002 7.398402692941118 NC_027314.1 103963436 144952805 1.394267163313071 4.679622334284693 NC_027315.1 87796322 130786916 1.4896628129820746 12.67701662986602 NC_027316.1 57682537 81431033 1.4117103240448665 11.311975944153476 NC_027317.1 70695409 106940548 1.5126943816111171 7.620188108105213 NC_027318.1 82978132 118946455 1.4334674947852526 12.852525588659013 NC_027319.1 86795997 121432659 1.399058288367838 5.639350440494655 NC_027320.1 58021487 79862922 1.3764370085861468 5.666288511746748 NC_027321.1 63420196 96232151 1.5173739135085613 14.376639616058018 NC_027322.1 49854004 72094425 1.4461110285143797 8.01250366086179 NC_027323.1 48650976 63909730 1.313637161153766 5.083429972831522 NC_027324.1 51481326 72824735 1.4145854557048512 5.9001228035156155 NC_027325.1 47900953 66144280 1.3808551992692086 7.9299634747217755 NC_027326.1 43943985 62016205 1.411255829438318 9.072556929029513 NC_027327.1 39600944 56896326 1.4367416594917535 10.334631160494725 NC_027328.1 42488238 55828070 1.3139652908176611 12.461927311287056 NC_001960.1 16665 10147196 608.8926492649265 1103.7889983823113