BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_16.deduplicated.sorted.bam outfile = zr3644_16/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 56,508,516 number of mapped reads = 56,508,516 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 28,254,258 number of mapped paired reads (second in pair) = 28,254,258 number of mapped paired reads (both in pair) = 56,508,516 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 24,793,306 number of mapped bases = 5,867,805,190 bp number of sequenced bases = 5,842,355,854 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,619,070 duplication rate = 16.93% >>>>>>> Insert size mean insert size = 151.7535 std insert size = 65.9729 median insert size = 130 >>>>>>> Mapping quality mean mapping quality = 24.6472 >>>>>>> ACTG content number of A's = 2,394,061,882 bp (40.98%) number of C's = 519,075,212 bp (8.88%) number of T's = 2,417,993,160 bp (41.39%) number of G's = 511,183,017 bp (8.75%) number of N's = 42,583 bp (0%) GC percentage = 17.63% >>>>>>> Mismatches and indels general error rate = 0.1954 number of mismatches = 1,113,920,479 number of insertions = 12,222,262 mapped reads with insertion percentage = 16.45% number of deletions = 10,800,068 mapped reads with deletion percentage = 15.86% homopolymer indels = 49.09% >>>>>>> Coverage mean coverageData = 10.4042X std coverageData = 12.3671X paired-end adapted mean coverage = 7.2118X There is a 83.28% of reference with a coverageData >= 1X There is a 77.89% of reference with a coverageData >= 2X There is a 72.26% of reference with a coverageData >= 3X There is a 67.69% of reference with a coverageData >= 4X There is a 63.05% of reference with a coverageData >= 5X There is a 58.76% of reference with a coverageData >= 6X There is a 54.51% of reference with a coverageData >= 7X There is a 50.47% of reference with a coverageData >= 8X There is a 46.56% of reference with a coverageData >= 9X There is a 42.85% of reference with a coverageData >= 10X There is a 39.31% of reference with a coverageData >= 11X There is a 35.97% of reference with a coverageData >= 12X There is a 32.82% of reference with a coverageData >= 13X There is a 29.87% of reference with a coverageData >= 14X There is a 27.12% of reference with a coverageData >= 15X There is a 24.55% of reference with a coverageData >= 16X There is a 22.18% of reference with a coverageData >= 17X There is a 19.99% of reference with a coverageData >= 18X There is a 17.98% of reference with a coverageData >= 19X There is a 16.14% of reference with a coverageData >= 20X There is a 14.47% of reference with a coverageData >= 21X There is a 12.95% of reference with a coverageData >= 22X There is a 11.57% of reference with a coverageData >= 23X There is a 10.33% of reference with a coverageData >= 24X There is a 9.21% of reference with a coverageData >= 25X There is a 8.2% of reference with a coverageData >= 26X There is a 7.31% of reference with a coverageData >= 27X There is a 6.51% of reference with a coverageData >= 28X There is a 5.8% of reference with a coverageData >= 29X There is a 5.17% of reference with a coverageData >= 30X There is a 4.61% of reference with a coverageData >= 31X There is a 4.12% of reference with a coverageData >= 32X There is a 3.68% of reference with a coverageData >= 33X There is a 3.3% of reference with a coverageData >= 34X There is a 2.97% of reference with a coverageData >= 35X There is a 2.67% of reference with a coverageData >= 36X There is a 2.41% of reference with a coverageData >= 37X There is a 2.18% of reference with a coverageData >= 38X There is a 1.98% of reference with a coverageData >= 39X There is a 1.8% of reference with a coverageData >= 40X There is a 1.65% of reference with a coverageData >= 41X There is a 1.51% of reference with a coverageData >= 42X There is a 1.39% of reference with a coverageData >= 43X There is a 1.28% of reference with a coverageData >= 44X There is a 1.18% of reference with a coverageData >= 45X There is a 1.09% of reference with a coverageData >= 46X There is a 1.02% of reference with a coverageData >= 47X There is a 0.95% of reference with a coverageData >= 48X There is a 0.88% of reference with a coverageData >= 49X There is a 0.83% of reference with a coverageData >= 50X There is a 0.78% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 591534766 7.776088601238283 17.24434821947177 NC_088854.1 61469542 722033591 11.74620092337763 10.899778313661727 NC_088855.1 61039741 723786080 11.85762043125314 10.915028789727792 NC_088856.1 57946171 544911686 9.403756565727182 11.948465704292307 NC_088857.1 57274926 658486493 11.496941838039215 11.095250033363627 NC_088858.1 56905015 678331491 11.920416697895607 10.819430980734191 NC_088859.1 53672946 660068509 12.297974271805389 11.860983292238675 NC_088860.1 51133819 540465791 10.569634765594175 11.68522231777803 NC_088861.1 50364239 400538330 7.952831968730829 10.762950220377114 NC_088862.1 37310742 344362621 9.229583828700056 11.649681751458525 NW_027062568.1 15579 133786 8.587585852750497 7.956893548897036 NW_027062569.1 16498 125749 7.622075403079161 16.042061957332795 NW_027062570.1 4000 63191 15.79775 14.71949709781214 NW_027062571.1 36893 10845 0.2939582034532296 1.4480090442590088 NW_027062572.1 51000 30583 0.5996666666666667 1.9182460755950859 NW_027062573.1 2000 45867 22.9335 12.428474936612295 NW_027062574.1 37061 4350 0.11737405898383746 0.5240560909442166 NW_027062575.1 49428 412191 8.339220684632192 16.020727011626725 NW_027062576.1 49232 181555 3.6877437439064025 7.082690856254129 NW_027062577.1 17087 156073 9.134020015216246 6.676070988691972 NW_027062578.1 34507 540939 15.676210623931377 9.780730022815376 NW_027062579.1 64000 415588 6.4935625 9.010004406452689 NW_027062580.1 24229 145612 6.009822939452722 7.900754962099014 NW_027062581.1 5000 15806 3.1612 5.744745397317447 NW_027062582.1 18808 185224 9.848149723521905 11.283709903765606 NW_027062583.1 1000 456 0.456 0.7809532636464234 NW_027062584.1 74000 10794 0.14586486486486486 1.1467275967526582 NW_027062585.1 39334 257195 6.538745106015153 6.523318654374376 NW_027062586.1 258015 550028 2.1317675328953745 4.910445544881602