BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_32psu_3_S3.sorted.bam outfile = /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_32psu_3_S3.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 = 28,590,284 number of mapped reads = 28,590,284 (100%) number of mapped paired reads (first in pair) = 14,295,142 number of mapped paired reads (second in pair) = 14,295,142 number of mapped paired reads (both in pair) = 28,590,284 number of mapped paired reads (singletons) = 0 number of mapped bases = 2,841,005,253 bp number of sequenced bases = 2,833,478,635 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,200,829 duplication rate = 20.03% >>>>>>> Insert size mean insert size = 112.6069 std insert size = 51.1898 median insert size = 103 >>>>>>> Mapping quality mean mapping quality = 23.5231 >>>>>>> ACTG content number of A's = 1,020,527,321 bp (36.02%) number of C's = 396,941,658 bp (14.01%) number of T's = 1,019,767,148 bp (35.99%) number of G's = 396,242,508 bp (13.98%) number of N's = 17,255 bp (0%) GC percentage = 27.99% >>>>>>> Mismatches and indels general error rate = 0.2097 number of mismatches = 575,497,392 number of insertions = 6,578,592 mapped reads with insertion percentage = 17.02% number of deletions = 4,585,598 mapped reads with deletion percentage = 13.83% homopolymer indels = 45.22% >>>>>>> Coverage mean coverageData = 1.2682X std coverageData = 10.7154X There is a 32.48% of reference with a coverageData >= 1X There is a 27.55% of reference with a coverageData >= 2X There is a 13.41% of reference with a coverageData >= 3X There is a 11.54% of reference with a coverageData >= 4X There is a 6.46% of reference with a coverageData >= 5X There is a 5.65% of reference with a coverageData >= 6X There is a 3.6% of reference with a coverageData >= 7X There is a 3.21% of reference with a coverageData >= 8X There is a 2.28% of reference with a coverageData >= 9X There is a 2.07% of reference with a coverageData >= 10X There is a 1.57% of reference with a coverageData >= 11X There is a 1.44% of reference with a coverageData >= 12X There is a 1.14% of reference with a coverageData >= 13X There is a 1.06% of reference with a coverageData >= 14X There is a 0.86% of reference with a coverageData >= 15X There is a 0.8% of reference with a coverageData >= 16X There is a 0.66% 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 0.48% of reference with a coverageData >= 20X There is a 0.41% of reference with a coverageData >= 21X There is a 0.38% of reference with a coverageData >= 22X There is a 0.33% of reference with a coverageData >= 23X There is a 0.31% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.15% of reference with a coverageData >= 31X There is a 0.14% of reference with a coverageData >= 32X There is a 0.13% 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 0.05% 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 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_027300.1 159038749 207715709 1.3060698119550727 5.638620054906873 NC_027301.1 72943711 88696168 1.2159536001671207 4.54305955577226 NC_027302.1 92503428 112845984 1.2199113745276553 3.97199363737827 NC_027303.1 82398023 106033471 1.286844843352613 9.469507536679028 NC_027304.1 80503876 98761548 1.2267924590363823 6.579310046534279 NC_027305.1 87043187 106183262 1.2198917073199538 8.472413268882987 NC_027306.1 58785265 74644098 1.269775648710608 7.9121543055372605 NC_027307.1 26434011 34447628 1.3031555445747527 14.495134470642865 NC_027308.1 141712163 178187998 1.2573938201761834 7.734601899505041 NC_027309.1 116138521 153122194 1.3184444978423653 15.916645924037775 NC_027310.1 93888508 116157430 1.2371847468275883 5.331677958340951 NC_027311.1 91880962 117811775 1.2822218274118635 10.679067478417513 NC_027312.1 107758822 138273214 1.2831730287474745 5.17105764476501 NC_027313.1 93901823 118284209 1.2596582816075892 7.71897639331528 NC_027314.1 103963436 128635495 1.2373147709354277 4.400425855770371 NC_027315.1 87796322 113789962 1.2960675277490554 6.123484298934364 NC_027316.1 57682537 71163723 1.2337134720686782 5.8019973907207785 NC_027317.1 70695409 93212208 1.3185044024570252 8.408583552426553 NC_027318.1 82978132 107914289 1.3005148031049916 31.830282165302794 NC_027319.1 86795997 110795767 1.276507797934506 7.988882051011324 NC_027320.1 58021487 70583350 1.2165036376954628 3.9431386780298143 NC_027321.1 63420196 86305290 1.3608486798117116 24.183501789468583 NC_027322.1 49854004 64124643 1.2862486030209328 5.456267262235604 NC_027323.1 48650976 58254212 1.1973904079539945 5.4907297690042505 NC_027324.1 51481326 64435123 1.2516212771986488 6.903714853090583 NC_027325.1 47900953 57800237 1.2066615250848975 5.666500117209798 NC_027326.1 43943985 55260800 1.2575281918560641 5.878791346363692 NC_027327.1 39600944 51445465 1.2990969356690083 12.037830593806296 NC_027328.1 42488238 49715643 1.170103664924867 6.633250295055638 NC_001960.1 16665 6404358 384.2999099909991 545.8597366313123