BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_14.deduplicated.sorted.bam outfile = zr3644_14/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 41,476,432 number of mapped reads = 41,476,432 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 20,738,216 number of mapped paired reads (second in pair) = 20,738,216 number of mapped paired reads (both in pair) = 41,476,432 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 17,489,279 number of mapped bases = 4,371,529,094 bp number of sequenced bases = 4,352,185,042 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,358,734 duplication rate = 13.95% >>>>>>> Insert size mean insert size = 161.0074 std insert size = 71.1968 median insert size = 139 >>>>>>> Mapping quality mean mapping quality = 24.5806 >>>>>>> ACTG content number of A's = 1,784,136,208 bp (40.99%) number of C's = 385,667,282 bp (8.86%) number of T's = 1,801,755,359 bp (41.4%) number of G's = 380,595,476 bp (8.74%) number of N's = 30,717 bp (0%) GC percentage = 17.61% >>>>>>> Mismatches and indels general error rate = 0.1946 number of mismatches = 825,828,598 number of insertions = 9,170,651 mapped reads with insertion percentage = 16.77% number of deletions = 8,192,534 mapped reads with deletion percentage = 16.35% homopolymer indels = 48.95% >>>>>>> Coverage mean coverageData = 7.7511X std coverageData = 9.1514X paired-end adapted mean coverage = 5.5348X There is a 79.39% of reference with a coverageData >= 1X There is a 73.01% of reference with a coverageData >= 2X There is a 66.51% of reference with a coverageData >= 3X There is a 61.09% of reference with a coverageData >= 4X There is a 55.63% of reference with a coverageData >= 5X There is a 50.54% of reference with a coverageData >= 6X There is a 45.58% of reference with a coverageData >= 7X There is a 40.93% of reference with a coverageData >= 8X There is a 36.51% of reference with a coverageData >= 9X There is a 32.43% of reference with a coverageData >= 10X There is a 28.64% of reference with a coverageData >= 11X There is a 25.19% of reference with a coverageData >= 12X There is a 22.04% of reference with a coverageData >= 13X There is a 19.22% of reference with a coverageData >= 14X There is a 16.69% of reference with a coverageData >= 15X There is a 14.46% of reference with a coverageData >= 16X There is a 12.48% of reference with a coverageData >= 17X There is a 10.76% of reference with a coverageData >= 18X There is a 9.25% of reference with a coverageData >= 19X There is a 7.95% of reference with a coverageData >= 20X There is a 6.83% of reference with a coverageData >= 21X There is a 5.87% of reference with a coverageData >= 22X There is a 5.05% of reference with a coverageData >= 23X There is a 4.36% of reference with a coverageData >= 24X There is a 3.77% of reference with a coverageData >= 25X There is a 3.27% of reference with a coverageData >= 26X There is a 2.84% of reference with a coverageData >= 27X There is a 2.49% of reference with a coverageData >= 28X There is a 2.19% of reference with a coverageData >= 29X There is a 1.93% of reference with a coverageData >= 30X There is a 1.71% of reference with a coverageData >= 31X There is a 1.53% of reference with a coverageData >= 32X There is a 1.37% of reference with a coverageData >= 33X There is a 1.24% of reference with a coverageData >= 34X There is a 1.12% of reference with a coverageData >= 35X There is a 1.02% of reference with a coverageData >= 36X There is a 0.93% of reference with a coverageData >= 37X There is a 0.85% of reference with a coverageData >= 38X There is a 0.79% of reference with a coverageData >= 39X There is a 0.73% of reference with a coverageData >= 40X There is a 0.67% of reference with a coverageData >= 41X There is a 0.62% of reference with a coverageData >= 42X There is a 0.58% of reference with a coverageData >= 43X There is a 0.54% of reference with a coverageData >= 44X There is a 0.5% of reference with a coverageData >= 45X There is a 0.47% of reference with a coverageData >= 46X There is a 0.44% of reference with a coverageData >= 47X There is a 0.41% of reference with a coverageData >= 48X There is a 0.39% of reference with a coverageData >= 49X There is a 0.37% of reference with a coverageData >= 50X There is a 0.34% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 457945471 6.019975091424798 10.147831899020836 NC_088854.1 61469542 533524983 8.679501516377005 9.459365933951918 NC_088855.1 61039741 530967936 8.698725245246372 8.376376153106378 NC_088856.1 57946171 411165770 7.095650375242223 8.66667990972964 NC_088857.1 57274926 491603133 8.583217252869083 8.697406462084576 NC_088858.1 56905015 500135993 8.788961623153952 8.357918146596495 NC_088859.1 53672946 484779961 9.032110162166243 8.194859862408602 NC_088860.1 51133819 404676686 7.914071233365143 9.297156947894075 NC_088861.1 50364239 300351171 5.96358005131379 8.429948310706486 NC_088862.1 37310742 254182247 6.812575504394954 11.053889939369816 NW_027062568.1 15579 85749 5.504140188715579 6.286165805044693 NW_027062569.1 16498 42580 2.5809188992605163 5.874538345759245 NW_027062570.1 4000 29802 7.4505 6.657129392613606 NW_027062571.1 36893 5016 0.135960751362047 0.6626813140747687 NW_027062572.1 51000 11807 0.23150980392156864 0.731816768580671 NW_027062573.1 2000 26085 13.0425 9.122147978957585 NW_027062574.1 37061 3517 0.09489760125198997 0.3721573863563914 NW_027062575.1 49428 201022 4.06696609209355 7.092793799447154 NW_027062576.1 49232 148741 3.0212260318492037 6.197984927371171 NW_027062577.1 17087 96270 5.634107801252414 5.321719619213233 NW_027062578.1 34507 426106 12.348393079664996 7.746778040669541 NW_027062579.1 64000 209269 3.269828125 6.760786143495161 NW_027062580.1 24229 175881 7.259110982706674 8.545695499345362 NW_027062581.1 5000 21694 4.3388 6.801860039724429 NW_027062582.1 18808 120487 6.406156954487452 6.3531054947097765 NW_027062583.1 1000 0 0.0 0.0 NW_027062584.1 74000 7394 0.09991891891891892 0.6341667707004429 NW_027062585.1 39334 204113 5.189225606345655 5.756747447692635 NW_027062586.1 258015 380210 1.4735964963277328 6.665691695814111