BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_32psu_4_S4.sorted.bam outfile = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_32psu_4_S4.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 = 31,221,158 number of mapped reads = 31,221,158 (100%) number of mapped paired reads (first in pair) = 15,610,579 number of mapped paired reads (second in pair) = 15,610,579 number of mapped paired reads (both in pair) = 31,221,158 number of mapped paired reads (singletons) = 0 number of mapped bases = 3,639,805,204 bp number of sequenced bases = 3,629,763,357 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,153,913 duplication rate = 25.74% >>>>>>> Insert size mean insert size = 143.5118 std insert size = 65.9516 median insert size = 133 >>>>>>> Mapping quality mean mapping quality = 24.5146 >>>>>>> ACTG content number of A's = 1,347,847,288 bp (37.13%) number of C's = 468,069,404 bp (12.9%) number of T's = 1,347,193,224 bp (37.12%) number of G's = 466,653,441 bp (12.86%) number of N's = 25,556 bp (0%) GC percentage = 25.75% >>>>>>> Mismatches and indels general error rate = 0.2109 number of mismatches = 740,419,680 number of insertions = 8,441,149 mapped reads with insertion percentage = 18.94% number of deletions = 6,089,037 mapped reads with deletion percentage = 16.62% homopolymer indels = 46.94% >>>>>>> Coverage mean coverageData = 1.6248X std coverageData = 8.5179X There is a 41.86% of reference with a coverageData >= 1X There is a 33.25% of reference with a coverageData >= 2X There is a 19.07% of reference with a coverageData >= 3X There is a 15.57% of reference with a coverageData >= 4X There is a 9.57% of reference with a coverageData >= 5X There is a 7.95% of reference with a coverageData >= 6X There is a 5.2% of reference with a coverageData >= 7X There is a 4.4% of reference with a coverageData >= 8X There is a 3.06% of reference with a coverageData >= 9X There is a 2.65% of reference with a coverageData >= 10X There is a 1.95% of reference with a coverageData >= 11X There is a 1.71% of reference with a coverageData >= 12X There is a 1.31% of reference with a coverageData >= 13X There is a 1.17% of reference with a coverageData >= 14X There is a 0.93% of reference with a coverageData >= 15X There is a 0.84% of reference with a coverageData >= 16X There is a 0.68% 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 0.47% of reference with a coverageData >= 20X There is a 0.4% of reference with a coverageData >= 21X There is a 0.37% of reference with a coverageData >= 22X There is a 0.31% of reference with a coverageData >= 23X There is a 0.29% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.16% of reference with a coverageData >= 30X There is a 0.14% of reference with a coverageData >= 31X There is a 0.13% of reference with a coverageData >= 32X There is a 0.12% of reference with a coverageData >= 33X There is a 0.12% of reference with a coverageData >= 34X There is a 0.11% of reference with a coverageData >= 35X There is a 0.1% of reference with a coverageData >= 36X There is a 0.09% of reference with a coverageData >= 37X There is a 0.09% of reference with a coverageData >= 38X There is a 0.08% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.07% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_027300.1 159038749 268401169 1.6876463798140162 6.249714269638322 NC_027301.1 72943711 113315447 1.553464245875837 4.900207557718881 NC_027302.1 92503428 147003245 1.5891653766604195 4.833750823032345 NC_027303.1 82398023 135834227 1.6485131809533828 5.792565149169485 NC_027304.1 80503876 126961687 1.5770878783525901 6.390555900004647 NC_027305.1 87043187 134220264 1.541996204711576 8.696143020586149 NC_027306.1 58785265 92508387 1.5736662410214532 5.9036743040894155 NC_027307.1 26434011 42812568 1.619601656366111 9.525258745195808 NC_027308.1 141712163 227427376 1.6048543130345134 5.721890617086204 NC_027309.1 116138521 198035188 1.705163681221668 16.4874590911074 NC_027310.1 93888508 149528077 1.592613198198868 5.340733274453253 NC_027311.1 91880962 152945097 1.6646005186580437 8.553124478641887 NC_027312.1 107758822 180379884 1.6739221963655095 5.318845688685953 NC_027313.1 93901823 151790426 1.6164800762174767 6.312468228587239 NC_027314.1 103963436 166926155 1.6056236829263704 4.526435342756992 NC_027315.1 87796322 145489074 1.65712037458699 6.547038631732097 NC_027316.1 57682537 91913017 1.5934288223141087 6.904757111360236 NC_027317.1 70695409 119848236 1.6952760822134858 7.634598926671957 NC_027318.1 82978132 133510071 1.6089789897897437 13.794661084339065 NC_027319.1 86795997 141374048 1.6288083884790217 5.407878951695912 NC_027320.1 58021487 90031003 1.5516838270622053 4.115075031130618 NC_027321.1 63420196 108376594 1.7088656427362665 13.041787520157824 NC_027322.1 49854004 81980667 1.6444148999546757 5.568322867570865 NC_027323.1 48650976 74369864 1.5286407409380647 4.790630623344602 NC_027324.1 51481326 82173418 1.5961791271654502 5.043492826024507 NC_027325.1 47900953 74829565 1.5621727818233595 7.151739328682222 NC_027326.1 43943985 69018837 1.5706094247028348 5.102104442027331 NC_027327.1 39600944 64656495 1.6327008517776749 9.700157695225759 NC_027328.1 42488238 62988955 1.4825033459848347 8.073462548023322 NC_001960.1 16665 11156163 669.4367236723673 1056.6341263776362