BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_26psu_1_S13.sorted.bam outfile = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_26psu_1_S13.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 = 43,151,604 number of mapped reads = 43,151,604 (100%) number of mapped paired reads (first in pair) = 21,575,802 number of mapped paired reads (second in pair) = 21,575,802 number of mapped paired reads (both in pair) = 43,151,604 number of mapped paired reads (singletons) = 0 number of mapped bases = 4,671,646,024 bp number of sequenced bases = 4,658,808,139 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,161,108 duplication rate = 21.99% >>>>>>> Insert size mean insert size = 126.8247 std insert size = 58.2802 median insert size = 116 >>>>>>> Mapping quality mean mapping quality = 23.5337 >>>>>>> ACTG content number of A's = 1,700,108,382 bp (36.49%) number of C's = 631,343,923 bp (13.55%) number of T's = 1,699,080,232 bp (36.47%) number of G's = 628,275,602 bp (13.49%) number of N's = 31,127 bp (0%) GC percentage = 27.04% >>>>>>> Mismatches and indels general error rate = 0.2116 number of mismatches = 952,291,310 number of insertions = 11,390,891 mapped reads with insertion percentage = 18.6% number of deletions = 7,804,249 mapped reads with deletion percentage = 15.41% homopolymer indels = 45.22% >>>>>>> Coverage mean coverageData = 2.0853X std coverageData = 15.4161X There is a 44.96% of reference with a coverageData >= 1X There is a 37.34% of reference with a coverageData >= 2X There is a 21.71% of reference with a coverageData >= 3X There is a 18.12% of reference with a coverageData >= 4X There is a 11.56% of reference with a coverageData >= 5X There is a 9.81% of reference with a coverageData >= 6X There is a 6.88% of reference with a coverageData >= 7X There is a 5.99% of reference with a coverageData >= 8X There is a 4.56% of reference with a coverageData >= 9X There is a 4.07% of reference with a coverageData >= 10X There is a 3.28% of reference with a coverageData >= 11X There is a 2.98% of reference with a coverageData >= 12X There is a 2.5% of reference with a coverageData >= 13X There is a 2.3% of reference with a coverageData >= 14X There is a 1.97% of reference with a coverageData >= 15X There is a 1.83% of reference with a coverageData >= 16X There is a 1.59% of reference with a coverageData >= 17X There is a 1.48% of reference with a coverageData >= 18X There is a 1.3% of reference with a coverageData >= 19X There is a 1.21% of reference with a coverageData >= 20X There is a 1.07% of reference with a coverageData >= 21X There is a 1% of reference with a coverageData >= 22X There is a 0.89% of reference with a coverageData >= 23X There is a 0.83% of reference with a coverageData >= 24X There is a 0.74% of reference with a coverageData >= 25X There is a 0.69% of reference with a coverageData >= 26X There is a 0.62% of reference with a coverageData >= 27X There is a 0.58% of reference with a coverageData >= 28X There is a 0.52% of reference with a coverageData >= 29X There is a 0.49% of reference with a coverageData >= 30X There is a 0.44% of reference with a coverageData >= 31X There is a 0.42% of reference with a coverageData >= 32X There is a 0.38% of reference with a coverageData >= 33X There is a 0.36% of reference with a coverageData >= 34X There is a 0.33% of reference with a coverageData >= 35X There is a 0.31% of reference with a coverageData >= 36X There is a 0.28% of reference with a coverageData >= 37X There is a 0.27% of reference with a coverageData >= 38X There is a 0.24% of reference with a coverageData >= 39X There is a 0.23% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_027300.1 159038749 345557754 2.172789689134187 13.233021421675115 NC_027301.1 72943711 145063271 1.9887015482390251 8.061344911297214 NC_027302.1 92503428 185545311 2.005820919415008 6.583525794345192 NC_027303.1 82398023 173148172 2.1013631844055287 10.409874860442502 NC_027304.1 80503876 162051440 2.0129644440970766 10.832379885468427 NC_027305.1 87043187 172439143 1.9810757044086633 16.148474260242885 NC_027306.1 58785265 120347279 2.047235459430182 10.476973950287906 NC_027307.1 26434011 55550751 2.1014877764861337 20.47400580181029 NC_027308.1 141712163 291028877 2.053661949962615 10.549008903590376 NC_027309.1 116138521 255270729 2.1979850165303896 31.761685063144597 NC_027310.1 93888508 192252615 2.04766929516017 9.025837652532395 NC_027311.1 91880962 193593164 2.106999750394429 13.093239633994441 NC_027312.1 107758822 228745300 2.122752418358842 9.408585049644953 NC_027313.1 93901823 195068025 2.0773614267318323 11.044503290581595 NC_027314.1 103963436 212010035 2.0392749908727525 6.7598727702481725 NC_027315.1 87796322 188620223 2.1483841088468374 11.904920537064708 NC_027316.1 57682537 116689703 2.022964125173621 10.836412045216473 NC_027317.1 70695409 153458485 2.1706994438634624 12.8544021198834 NC_027318.1 82978132 174299540 2.1005478889305436 28.52640576525096 NC_027319.1 86795997 180213078 2.0762832875806474 10.280980242541409 NC_027320.1 58021487 116040481 1.9999570331591123 5.9640447462477875 NC_027321.1 63420196 141423755 2.2299482486619877 29.40964019352262 NC_027322.1 49854004 105610619 2.1183979324910394 9.77548998161684 NC_027323.1 48650976 94735215 1.9472418189513814 7.8010878067304015 NC_027324.1 51481326 106433962 2.067428527384862 9.6266138468952 NC_027325.1 47900953 94641048 1.9757654508460405 9.812602024403102 NC_027326.1 43943985 90053420 2.0492775063526896 9.215314480623677 NC_027327.1 39600944 83249681 2.10221455831962 15.941846718951663 NC_027328.1 42488238 81841805 1.9262226171864316 14.892448485005492 NC_001960.1 16665 16663143 999.8885688568857 1423.3049802263079