BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/8C_26psu_4_S12.sorted.bam outfile = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/8C_26psu_4_S12.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 = 25,557,502 number of mapped reads = 25,557,502 (100%) number of mapped paired reads (first in pair) = 12,778,751 number of mapped paired reads (second in pair) = 12,778,751 number of mapped paired reads (both in pair) = 25,557,502 number of mapped paired reads (singletons) = 0 number of mapped bases = 3,001,947,480 bp number of sequenced bases = 2,992,688,627 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,808,795 duplication rate = 43.44% >>>>>>> Insert size mean insert size = 154.6536 std insert size = 80.3545 median insert size = 139 >>>>>>> Mapping quality mean mapping quality = 23.7412 >>>>>>> ACTG content number of A's = 1,116,622,296 bp (37.31%) number of C's = 381,649,756 bp (12.75%) number of T's = 1,114,662,567 bp (37.25%) number of G's = 379,754,008 bp (12.69%) number of N's = 21,014 bp (0%) GC percentage = 25.44% >>>>>>> Mismatches and indels general error rate = 0.2047 number of mismatches = 595,597,068 number of insertions = 6,060,286 mapped reads with insertion percentage = 16.95% number of deletions = 5,322,998 mapped reads with deletion percentage = 17.4% homopolymer indels = 44.7% >>>>>>> Coverage mean coverageData = 1.34X std coverageData = 13.3278X There is a 26.96% of reference with a coverageData >= 1X There is a 21.86% of reference with a coverageData >= 2X There is a 13.59% of reference with a coverageData >= 3X There is a 11.71% of reference with a coverageData >= 4X There is a 7.85% of reference with a coverageData >= 5X There is a 6.97% of reference with a coverageData >= 6X There is a 4.85% of reference with a coverageData >= 7X There is a 4.38% of reference with a coverageData >= 8X There is a 3.14% of reference with a coverageData >= 9X There is a 2.85% of reference with a coverageData >= 10X There is a 2.1% of reference with a coverageData >= 11X There is a 1.92% of reference with a coverageData >= 12X There is a 1.45% of reference with a coverageData >= 13X There is a 1.33% of reference with a coverageData >= 14X There is a 1.04% of reference with a coverageData >= 15X There is a 0.96% of reference with a coverageData >= 16X There is a 0.77% of reference with a coverageData >= 17X There is a 0.71% of reference with a coverageData >= 18X There is a 0.58% of reference with a coverageData >= 19X There is a 0.54% of reference with a coverageData >= 20X There is a 0.46% of reference with a coverageData >= 21X There is a 0.43% of reference with a coverageData >= 22X There is a 0.37% of reference with a coverageData >= 23X There is a 0.35% of reference with a coverageData >= 24X There is a 0.31% of reference with a coverageData >= 25X There is a 0.29% of reference with a coverageData >= 26X There is a 0.26% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.14% of reference with a coverageData >= 39X There is a 0.13% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.12% of reference with a coverageData >= 42X There is a 0.12% of reference with a coverageData >= 43X There is a 0.11% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.1% 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 0.1% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_027300.1 159038749 216553533 1.3616400679811684 14.374447379077097 NC_027301.1 72943711 99273706 1.360963195305487 9.31888317354846 NC_027302.1 92503428 120599983 1.3037352842750864 9.763598098957544 NC_027303.1 82398023 105882237 1.2850094352385129 9.718396763584867 NC_027304.1 80503876 111124091 1.3803570277783892 10.117938734385412 NC_027305.1 87043187 119680826 1.3749591452803767 14.819319101036116 NC_027306.1 58785265 84603391 1.4391938353939546 11.233953050077668 NC_027307.1 26434011 37673937 1.4252069805070444 20.027597233179936 NC_027308.1 141712163 189126784 1.3345839905075756 11.763510377848494 NC_027309.1 116138521 155092578 1.3354103071452064 16.6515323874078 NC_027310.1 93888508 122022643 1.2996547245164445 9.676056746792526 NC_027311.1 91880962 122529985 1.3335731617611928 17.69689800109236 NC_027312.1 107758822 138519715 1.2854605537540118 8.874881850840634 NC_027313.1 93901823 129527868 1.3793967343956677 26.809808747554186 NC_027314.1 103963436 142105467 1.3668792843668613 10.330062200069428 NC_027315.1 87796322 125121792 1.4251370575637554 12.459116826123616 NC_027316.1 57682537 88314169 1.531038223925553 13.96712878867223 NC_027317.1 70695409 106976751 1.5132064799285623 15.564826531237344 NC_027318.1 82978132 106343042 1.2815791273778012 10.059950472602301 NC_027319.1 86795997 111843767 1.2885820874895877 9.648954800701791 NC_027320.1 58021487 69434165 1.1966974407257092 5.971946187276669 NC_027321.1 63420196 81247497 1.2810981694222452 12.581851203952626 NC_027322.1 49854004 60268685 1.2089036018049824 6.115760831608789 NC_027323.1 48650976 57497267 1.181831727281278 10.57837128029171 NC_027324.1 51481326 65556214 1.27339793073706 9.800601879245816 NC_027325.1 47900953 70098881 1.4634130765623807 18.01715442265301 NC_027326.1 43943985 56551534 1.2869004483776334 5.24995487561741 NC_027327.1 39600944 52113816 1.3159740838501224 19.060111432403723 NC_027328.1 42488238 51668442 1.216064596512569 6.9987376986671785 NC_001960.1 16665 4594714 275.7104110411041 421.59546584435554