BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_32psu_1_S1.sorted.bam outfile = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_32psu_1_S1.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 = 39,383,180 number of mapped reads = 39,383,180 (100%) number of mapped paired reads (first in pair) = 19,691,590 number of mapped paired reads (second in pair) = 19,691,590 number of mapped paired reads (both in pair) = 39,383,180 number of mapped paired reads (singletons) = 0 number of mapped bases = 3,955,683,671 bp number of sequenced bases = 3,945,071,014 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,512,260 duplication rate = 25.12% >>>>>>> Insert size mean insert size = 114.3008 std insert size = 52.5076 median insert size = 104 >>>>>>> Mapping quality mean mapping quality = 23.5487 >>>>>>> ACTG content number of A's = 1,428,843,411 bp (36.22%) number of C's = 544,870,442 bp (13.81%) number of T's = 1,428,060,144 bp (36.2%) number of G's = 543,297,017 bp (13.77%) number of N's = 24,416 bp (0%) GC percentage = 27.58% >>>>>>> Mismatches and indels general error rate = 0.2124 number of mismatches = 810,860,900 number of insertions = 9,445,805 mapped reads with insertion percentage = 17.33% number of deletions = 6,523,318 mapped reads with deletion percentage = 14.27% homopolymer indels = 44.91% >>>>>>> Coverage mean coverageData = 1.7658X std coverageData = 12.6447X There is a 36.66% of reference with a coverageData >= 1X There is a 30.75% of reference with a coverageData >= 2X There is a 16.84% of reference with a coverageData >= 3X There is a 14.56% of reference with a coverageData >= 4X There is a 9.21% of reference with a coverageData >= 5X There is a 8.15% of reference with a coverageData >= 6X There is a 5.81% of reference with a coverageData >= 7X There is a 5.26% of reference with a coverageData >= 8X There is a 4.1% of reference with a coverageData >= 9X There is a 3.78% of reference with a coverageData >= 10X There is a 3.1% of reference with a coverageData >= 11X There is a 2.89% of reference with a coverageData >= 12X There is a 2.45% of reference with a coverageData >= 13X There is a 2.3% of reference with a coverageData >= 14X There is a 1.98% of reference with a coverageData >= 15X There is a 1.86% of reference with a coverageData >= 16X There is a 1.62% of reference with a coverageData >= 17X There is a 1.53% of reference with a coverageData >= 18X There is a 1.34% of reference with a coverageData >= 19X There is a 1.27% of reference with a coverageData >= 20X There is a 1.12% of reference with a coverageData >= 21X There is a 1.05% of reference with a coverageData >= 22X There is a 0.93% of reference with a coverageData >= 23X There is a 0.88% of reference with a coverageData >= 24X There is a 0.78% of reference with a coverageData >= 25X There is a 0.74% of reference with a coverageData >= 26X There is a 0.66% of reference with a coverageData >= 27X There is a 0.62% of reference with a coverageData >= 28X There is a 0.56% of reference with a coverageData >= 29X There is a 0.53% of reference with a coverageData >= 30X There is a 0.47% of reference with a coverageData >= 31X There is a 0.45% of reference with a coverageData >= 32X There is a 0.4% of reference with a coverageData >= 33X There is a 0.38% of reference with a coverageData >= 34X There is a 0.35% of reference with a coverageData >= 35X There is a 0.33% of reference with a coverageData >= 36X There is a 0.3% of reference with a coverageData >= 37X There is a 0.28% of reference with a coverageData >= 38X There is a 0.26% of reference with a coverageData >= 39X There is a 0.24% of reference with a coverageData >= 40X There is a 0.22% of reference with a coverageData >= 41X There is a 0.21% 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 292129121 1.8368424225972753 10.242974509078483 NC_027301.1 72943711 120848732 1.6567395645664367 6.318942752732623 NC_027302.1 92503428 156260445 1.6892395058051255 5.521336890388571 NC_027303.1 82398023 148823154 1.8061495723022383 9.49890963752247 NC_027304.1 80503876 136262231 1.6926170238064064 8.525481982279501 NC_027305.1 87043187 144898593 1.6646747206073693 13.24933914980467 NC_027306.1 58785265 102545331 1.7444053539607247 12.058689900570513 NC_027307.1 26434011 46872759 1.773198891382772 17.67587544201726 NC_027308.1 141712163 247543278 1.7468033283776778 9.339589266361333 NC_027309.1 116138521 215585168 1.8562761618085355 20.002232678928213 NC_027310.1 93888508 160786573 1.7125266598122957 8.494722599672059 NC_027311.1 91880962 165966402 1.806319811932313 13.92309091678434 NC_027312.1 107758822 197160546 1.8296464488076902 8.14223478110392 NC_027313.1 93901823 165740920 1.765044753178008 10.03033009062477 NC_027314.1 103963436 179108555 1.7228033421288615 5.837012261730504 NC_027315.1 87796322 158221745 1.8021454816751892 8.88708883824454 NC_027316.1 57682537 95529800 1.656130346694009 8.193762171784124 NC_027317.1 70695409 127631743 1.8053752684279682 10.799866959019404 NC_027318.1 82978132 148308273 1.787317566994639 26.323482024050847 NC_027319.1 86795997 154942186 1.7851305515852303 9.542489969324926 NC_027320.1 58021487 99312774 1.7116550977054414 5.797561888079387 NC_027321.1 63420196 121904392 1.9221699031015294 25.563210795785743 NC_027322.1 49854004 90975648 1.8248413507569021 8.732603078930095 NC_027323.1 48650976 80784316 1.6604870578547077 6.343562862752806 NC_027324.1 51481326 90251939 1.7531005126014043 8.812904829032515 NC_027325.1 47900953 77337302 1.6145253310513468 6.986106404312842 NC_027326.1 43943985 77203360 1.7568584187346687 8.125670189756221 NC_027327.1 39600944 71107246 1.7955947211763437 12.234324648282657 NC_027328.1 42488238 68765866 1.6184682923306917 9.328313961912071 NC_001960.1 16665 12875273 772.5936393639364 1212.8220355076012