BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_13.deduplicated.sorted.bam outfile = zr3644_13/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 59,496,470 number of mapped reads = 59,496,470 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 29,748,235 number of mapped paired reads (second in pair) = 29,748,235 number of mapped paired reads (both in pair) = 59,496,470 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 24,701,129 number of mapped bases = 6,311,359,720 bp number of sequenced bases = 6,283,130,921 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,412,608 duplication rate = 17.33% >>>>>>> Insert size mean insert size = 164.6084 std insert size = 73.0305 median insert size = 142 >>>>>>> Mapping quality mean mapping quality = 24.7074 >>>>>>> ACTG content number of A's = 2,578,394,900 bp (41.04%) number of C's = 554,351,359 bp (8.82%) number of T's = 2,604,222,643 bp (41.45%) number of G's = 546,114,941 bp (8.69%) number of N's = 47,078 bp (0%) GC percentage = 17.51% >>>>>>> Mismatches and indels general error rate = 0.1943 number of mismatches = 1,190,067,209 number of insertions = 13,337,622 mapped reads with insertion percentage = 16.96% number of deletions = 11,922,223 mapped reads with deletion percentage = 16.57% homopolymer indels = 49.02% >>>>>>> Coverage mean coverageData = 11.1906X std coverageData = 12.4682X paired-end adapted mean coverage = 8.069X There is a 84.82% of reference with a coverageData >= 1X There is a 79.69% of reference with a coverageData >= 2X There is a 74.64% of reference with a coverageData >= 3X There is a 70.41% of reference with a coverageData >= 4X There is a 66.17% of reference with a coverageData >= 5X There is a 62.15% of reference with a coverageData >= 6X There is a 58.16% of reference with a coverageData >= 7X There is a 54.29% of reference with a coverageData >= 8X There is a 50.49% of reference with a coverageData >= 9X There is a 46.82% of reference with a coverageData >= 10X There is a 43.25% of reference with a coverageData >= 11X There is a 39.82% of reference with a coverageData >= 12X There is a 36.53% of reference with a coverageData >= 13X There is a 33.4% of reference with a coverageData >= 14X There is a 30.44% of reference with a coverageData >= 15X There is a 27.64% of reference with a coverageData >= 16X There is a 25.02% of reference with a coverageData >= 17X There is a 22.59% of reference with a coverageData >= 18X There is a 20.33% of reference with a coverageData >= 19X There is a 18.25% of reference with a coverageData >= 20X There is a 16.33% of reference with a coverageData >= 21X There is a 14.59% of reference with a coverageData >= 22X There is a 13.01% of reference with a coverageData >= 23X There is a 11.58% of reference with a coverageData >= 24X There is a 10.3% of reference with a coverageData >= 25X There is a 9.15% of reference with a coverageData >= 26X There is a 8.12% of reference with a coverageData >= 27X There is a 7.21% of reference with a coverageData >= 28X There is a 6.4% of reference with a coverageData >= 29X There is a 5.69% of reference with a coverageData >= 30X There is a 5.06% of reference with a coverageData >= 31X There is a 4.51% of reference with a coverageData >= 32X There is a 4.03% of reference with a coverageData >= 33X There is a 3.6% of reference with a coverageData >= 34X There is a 3.23% of reference with a coverageData >= 35X There is a 2.91% of reference with a coverageData >= 36X There is a 2.62% of reference with a coverageData >= 37X There is a 2.37% of reference with a coverageData >= 38X There is a 2.16% of reference with a coverageData >= 39X There is a 1.97% of reference with a coverageData >= 40X There is a 1.8% of reference with a coverageData >= 41X There is a 1.65% of reference with a coverageData >= 42X There is a 1.52% of reference with a coverageData >= 43X There is a 1.4% of reference with a coverageData >= 44X There is a 1.3% of reference with a coverageData >= 45X There is a 1.21% of reference with a coverageData >= 46X There is a 1.13% of reference with a coverageData >= 47X There is a 1.05% of reference with a coverageData >= 48X There is a 0.98% of reference with a coverageData >= 49X There is a 0.92% of reference with a coverageData >= 50X There is a 0.87% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 665839824 8.752874324984145 17.08532686928539 NC_088854.1 61469542 767554533 12.486745598332261 11.264713667571105 NC_088855.1 61039741 769055400 12.599257260937591 11.043567167163797 NC_088856.1 57946171 586802011 10.126674478629486 11.909985949970467 NC_088857.1 57274926 699421775 12.211657418815347 11.100875809258596 NC_088858.1 56905015 722509007 12.696754530334452 10.863578290456834 NC_088859.1 53672946 703438002 13.10600692572381 11.74072859641005 NC_088860.1 51133819 581848010 11.378927320097096 12.228832193594245 NC_088861.1 50364239 437754595 8.6917742368747 11.365156791122 NC_088862.1 37310742 373273087 10.004440195802056 11.677557276695875 NW_027062568.1 15579 150202 9.641312022594517 8.565733503622036 NW_027062569.1 16498 238539 14.458661655958299 16.562759692759865 NW_027062570.1 4000 65344 16.336 16.388075970046025 NW_027062571.1 36893 7370 0.1997668934486217 1.1008687088230782 NW_027062572.1 51000 51298 1.005843137254902 3.0454692590919086 NW_027062573.1 2000 44900 22.45 11.779959677350345 NW_027062574.1 37061 3464 0.0934675265103478 0.6785231496611168 NW_027062575.1 49428 438336 8.868171886380189 17.226048755021605 NW_027062576.1 49232 213208 4.330679233019175 9.380666483716615 NW_027062577.1 17087 161989 9.480248141862235 6.467689186932433 NW_027062578.1 34507 594109 17.217057408641725 8.982017683271946 NW_027062579.1 64000 476636 7.4474375 10.90060742286869 NW_027062580.1 24229 309862 12.788889347476164 12.188930487469928 NW_027062581.1 5000 51367 10.2734 12.531297029437933 NW_027062582.1 18808 204445 10.870108464483199 11.564513087393403 NW_027062583.1 1000 0 0.0 0.0 NW_027062584.1 74000 16597 0.22428378378378377 1.338324841130562 NW_027062585.1 39334 328076 8.340773885188387 7.95282808328824 NW_027062586.1 258015 507734 1.9678468306106234 5.824201624539297