BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/8C_26psu_2_S10.sorted.bam outfile = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/8C_26psu_2_S10.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 = 38,997,124 number of mapped reads = 38,997,124 (100%) number of mapped paired reads (first in pair) = 19,498,562 number of mapped paired reads (second in pair) = 19,498,562 number of mapped paired reads (both in pair) = 38,997,124 number of mapped paired reads (singletons) = 0 number of mapped bases = 4,147,494,626 bp number of sequenced bases = 4,136,477,171 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,481,258 duplication rate = 26.57% >>>>>>> Insert size mean insert size = 124.8789 std insert size = 59.3967 median insert size = 113 >>>>>>> Mapping quality mean mapping quality = 24.2685 >>>>>>> ACTG content number of A's = 1,510,679,015 bp (36.52%) number of C's = 560,826,315 bp (13.56%) number of T's = 1,507,996,841 bp (36.46%) number of G's = 556,975,000 bp (13.46%) number of N's = 26,257 bp (0%) GC percentage = 27.02% >>>>>>> Mismatches and indels general error rate = 0.2087 number of mismatches = 837,616,880 number of insertions = 8,865,838 mapped reads with insertion percentage = 16.46% number of deletions = 6,689,920 mapped reads with deletion percentage = 14.79% homopolymer indels = 46.59% >>>>>>> Coverage mean coverageData = 1.8514X std coverageData = 12.4513X There is a 41.15% of reference with a coverageData >= 1X There is a 33.97% of reference with a coverageData >= 2X There is a 19.62% of reference with a coverageData >= 3X There is a 16.62% of reference with a coverageData >= 4X There is a 10.5% of reference with a coverageData >= 5X There is a 9.05% of reference with a coverageData >= 6X There is a 6.21% of reference with a coverageData >= 7X There is a 5.46% of reference with a coverageData >= 8X There is a 4.04% of reference with a coverageData >= 9X There is a 3.62% of reference with a coverageData >= 10X There is a 2.84% of reference with a coverageData >= 11X There is a 2.59% of reference with a coverageData >= 12X There is a 2.11% of reference with a coverageData >= 13X There is a 1.95% of reference with a coverageData >= 14X There is a 1.64% of reference with a coverageData >= 15X There is a 1.52% of reference with a coverageData >= 16X There is a 1.3% of reference with a coverageData >= 17X There is a 1.21% of reference with a coverageData >= 18X There is a 1.05% of reference with a coverageData >= 19X There is a 0.98% of reference with a coverageData >= 20X There is a 0.86% of reference with a coverageData >= 21X There is a 0.8% of reference with a coverageData >= 22X There is a 0.71% of reference with a coverageData >= 23X There is a 0.66% of reference with a coverageData >= 24X There is a 0.59% of reference with a coverageData >= 25X There is a 0.55% of reference with a coverageData >= 26X There is a 0.49% of reference with a coverageData >= 27X There is a 0.46% of reference with a coverageData >= 28X There is a 0.41% of reference with a coverageData >= 29X There is a 0.39% of reference with a coverageData >= 30X There is a 0.35% of reference with a coverageData >= 31X There is a 0.33% of reference with a coverageData >= 32X There is a 0.3% of reference with a coverageData >= 33X There is a 0.28% of reference with a coverageData >= 34X There is a 0.26% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.22% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.11% 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 305629318 1.9217286348247118 7.895686382805051 NC_027301.1 72943711 128627781 1.763384111345802 6.238429076382093 NC_027302.1 92503428 165885993 1.7932956279198649 5.532427556090791 NC_027303.1 82398023 154330887 1.8729925959509974 9.018157651634478 NC_027304.1 80503876 143076856 1.777266674712656 7.573521425844308 NC_027305.1 87043187 153194338 1.7599808012544393 11.12520649796317 NC_027306.1 58785265 106565244 1.8127883577627828 7.967088237204694 NC_027307.1 26434011 47324125 1.7902740904511238 11.469716324638291 NC_027308.1 141712163 259616060 1.8319956064745127 6.959256526993095 NC_027309.1 116138521 225666999 1.943084835736801 21.36670110764199 NC_027310.1 93888508 170123747 1.8119762537924238 6.769837629814367 NC_027311.1 91880962 173339113 1.8865617993856008 11.94417220293351 NC_027312.1 107758822 205911073 1.9108511876642453 6.789518554718685 NC_027313.1 93901823 174278198 1.855961816630546 8.627252679441899 NC_027314.1 103963436 189213779 1.8200031307160722 5.731599028527513 NC_027315.1 87796322 166432377 1.8956645700944055 8.632798464315233 NC_027316.1 57682537 102133353 1.7706113203724032 8.396961782224489 NC_027317.1 70695409 135914854 1.9225414482006886 9.842401401468713 NC_027318.1 82978132 154235491 1.8587486519942387 27.668390815508534 NC_027319.1 86795997 161458667 1.8602086799002955 7.553343173553328 NC_027320.1 58021487 102066498 1.7591155152573046 5.171118714188747 NC_027321.1 63420196 124844674 1.9685318222605304 22.571167665226778 NC_027322.1 49854004 93011580 1.8656792341092603 7.210015696874469 NC_027323.1 48650976 84956928 1.7462533125748598 6.236811073093124 NC_027324.1 51481326 93835373 1.8227069947654417 6.121327636715697 NC_027325.1 47900953 83114816 1.735139090030213 8.742512626441217 NC_027326.1 43943985 79044929 1.7987656103560021 7.315751302086126 NC_027327.1 39600944 73697890 1.8610134647295276 13.161451779336995 NC_027328.1 42488238 71561653 1.6842697266005713 9.302134136037472 NC_001960.1 16665 18402032 1104.2323432343235 1676.5149840357342