BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_32psu_2_S2.sorted.bam outfile = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_32psu_2_S2.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 = 38,429,850 number of mapped reads = 38,429,850 (100%) number of mapped paired reads (first in pair) = 19,214,925 number of mapped paired reads (second in pair) = 19,214,925 number of mapped paired reads (both in pair) = 38,429,850 number of mapped paired reads (singletons) = 0 number of mapped bases = 3,961,421,499 bp number of sequenced bases = 3,950,703,163 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,418,542 duplication rate = 26.77% >>>>>>> Insert size mean insert size = 118.6843 std insert size = 54.9915 median insert size = 108 >>>>>>> Mapping quality mean mapping quality = 23.9112 >>>>>>> ACTG content number of A's = 1,432,176,979 bp (36.25%) number of C's = 546,236,321 bp (13.83%) number of T's = 1,429,811,033 bp (36.19%) number of G's = 542,478,830 bp (13.73%) number of N's = 24,652 bp (0%) GC percentage = 27.56% >>>>>>> Mismatches and indels general error rate = 0.2064 number of mismatches = 789,112,360 number of insertions = 9,083,145 mapped reads with insertion percentage = 17.6% number of deletions = 6,471,563 mapped reads with deletion percentage = 14.52% homopolymer indels = 45.86% >>>>>>> Coverage mean coverageData = 1.7683X std coverageData = 13.8162X There is a 39.55% of reference with a coverageData >= 1X There is a 33.42% of reference with a coverageData >= 2X There is a 18.87% of reference with a coverageData >= 3X There is a 16.28% of reference with a coverageData >= 4X There is a 10.04% of reference with a coverageData >= 5X There is a 8.76% of reference with a coverageData >= 6X There is a 5.85% of reference with a coverageData >= 7X There is a 5.18% of reference with a coverageData >= 8X There is a 3.72% of reference with a coverageData >= 9X There is a 3.35% of reference with a coverageData >= 10X There is a 2.56% of reference with a coverageData >= 11X There is a 2.33% of reference with a coverageData >= 12X There is a 1.86% of reference with a coverageData >= 13X There is a 1.72% of reference with a coverageData >= 14X There is a 1.42% of reference with a coverageData >= 15X There is a 1.32% of reference with a coverageData >= 16X There is a 1.11% of reference with a coverageData >= 17X There is a 1.04% of reference with a coverageData >= 18X There is a 0.89% of reference with a coverageData >= 19X There is a 0.83% of reference with a coverageData >= 20X There is a 0.72% of reference with a coverageData >= 21X There is a 0.68% of reference with a coverageData >= 22X There is a 0.59% of reference with a coverageData >= 23X There is a 0.56% of reference with a coverageData >= 24X There is a 0.49% of reference with a coverageData >= 25X There is a 0.47% of reference with a coverageData >= 26X There is a 0.41% of reference with a coverageData >= 27X There is a 0.39% of reference with a coverageData >= 28X There is a 0.35% of reference with a coverageData >= 29X There is a 0.33% of reference with a coverageData >= 30X There is a 0.3% of reference with a coverageData >= 31X There is a 0.28% of reference with a coverageData >= 32X There is a 0.26% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_027300.1 159038749 289425468 1.819842458645094 8.036587988954837 NC_027301.1 72943711 123249000 1.6896453211710054 6.459364421575378 NC_027302.1 92503428 157713897 1.7049519181062134 5.477723674950902 NC_027303.1 82398023 146619640 1.7794072559240894 8.438608939014681 NC_027304.1 80503876 137834549 1.7121479840299862 9.030209196786974 NC_027305.1 87043187 146157345 1.679135955810074 10.66962433031007 NC_027306.1 58785265 103115710 1.754108108554074 8.936956067137727 NC_027307.1 26434011 46382808 1.7546640197736167 15.724272570935558 NC_027308.1 141712163 247513233 1.7465913141132423 8.854827914987753 NC_027309.1 116138521 214893762 1.850322874354496 30.24465541806322 NC_027310.1 93888508 161810845 1.7234361099869646 6.683536274897494 NC_027311.1 91880962 163878923 1.7836004263864804 12.605739395005054 NC_027312.1 107758822 193250333 1.7933597399570682 7.676408983859028 NC_027313.1 93901823 164751582 1.754508876787195 8.447730493811301 NC_027314.1 103963436 179534321 1.7268986858033435 5.6866674064799305 NC_027315.1 87796322 157722485 1.7964589108869504 8.932485303051527 NC_027316.1 57682537 99806142 1.7302661635704408 8.92383254965617 NC_027317.1 70695409 129736415 1.835146253980934 9.840442323698493 NC_027318.1 82978132 146699330 1.7679276029014488 23.410794145519883 NC_027319.1 86795997 153787134 1.7718228871776196 8.592290532857167 NC_027320.1 58021487 97820901 1.6859426749955582 5.360599311355641 NC_027321.1 63420196 118694248 1.8715528409909046 19.72043478212218 NC_027322.1 49854004 89170940 1.788641490059655 7.728397131287893 NC_027323.1 48650976 80606521 1.656832557685996 6.176806253151747 NC_027324.1 51481326 90208913 1.7522647532427584 8.30936054999401 NC_027325.1 47900953 80126334 1.6727503104165797 7.273366834520392 NC_027326.1 43943985 77183241 1.7564005858822316 8.329363865757275 NC_027327.1 39600944 71465046 1.8046298593286059 12.436296552117046 NC_027328.1 42488238 68955185 1.6229240901917372 9.966960444651127 NC_001960.1 16665 23307248 1398.5747374737473 2079.6291526013133