BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_10.deduplicated.sorted.bam outfile = zr3644_10/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 57,723,916 number of mapped reads = 57,723,916 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 28,861,958 number of mapped paired reads (second in pair) = 28,861,958 number of mapped paired reads (both in pair) = 57,723,916 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 24,506,296 number of mapped bases = 6,074,173,231 bp number of sequenced bases = 6,047,211,950 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,912,649 duplication rate = 17.08% >>>>>>> Insert size mean insert size = 159.6215 std insert size = 70.5128 median insert size = 137 >>>>>>> Mapping quality mean mapping quality = 24.6704 >>>>>>> ACTG content number of A's = 2,475,984,566 bp (40.94%) number of C's = 539,185,855 bp (8.92%) number of T's = 2,501,043,116 bp (41.36%) number of G's = 530,951,086 bp (8.78%) number of N's = 47,327 bp (0%) GC percentage = 17.7% >>>>>>> Mismatches and indels general error rate = 0.1949 number of mismatches = 1,149,142,311 number of insertions = 12,803,428 mapped reads with insertion percentage = 16.77% number of deletions = 11,431,570 mapped reads with deletion percentage = 16.39% homopolymer indels = 48.96% >>>>>>> Coverage mean coverageData = 10.7701X std coverageData = 11.6988X paired-end adapted mean coverage = 7.6525X There is a 84.17% of reference with a coverageData >= 1X There is a 78.91% of reference with a coverageData >= 2X There is a 73.63% of reference with a coverageData >= 3X There is a 69.25% of reference with a coverageData >= 4X There is a 64.83% of reference with a coverageData >= 5X There is a 60.66% of reference with a coverageData >= 6X There is a 56.53% of reference with a coverageData >= 7X There is a 52.54% of reference with a coverageData >= 8X There is a 48.65% of reference with a coverageData >= 9X There is a 44.91% of reference with a coverageData >= 10X There is a 41.31% of reference with a coverageData >= 11X There is a 37.87% of reference with a coverageData >= 12X There is a 34.6% of reference with a coverageData >= 13X There is a 31.52% of reference with a coverageData >= 14X There is a 28.61% of reference with a coverageData >= 15X There is a 25.9% of reference with a coverageData >= 16X There is a 23.38% of reference with a coverageData >= 17X There is a 21.05% of reference with a coverageData >= 18X There is a 18.9% of reference with a coverageData >= 19X There is a 16.93% of reference with a coverageData >= 20X There is a 15.14% of reference with a coverageData >= 21X There is a 13.51% of reference with a coverageData >= 22X There is a 12.04% of reference with a coverageData >= 23X There is a 10.71% of reference with a coverageData >= 24X There is a 9.52% of reference with a coverageData >= 25X There is a 8.46% of reference with a coverageData >= 26X There is a 7.51% of reference with a coverageData >= 27X There is a 6.68% of reference with a coverageData >= 28X There is a 5.94% of reference with a coverageData >= 29X There is a 5.28% of reference with a coverageData >= 30X There is a 4.71% of reference with a coverageData >= 31X There is a 4.2% of reference with a coverageData >= 32X There is a 3.76% of reference with a coverageData >= 33X There is a 3.37% of reference with a coverageData >= 34X There is a 3.02% of reference with a coverageData >= 35X There is a 2.73% of reference with a coverageData >= 36X There is a 2.47% of reference with a coverageData >= 37X There is a 2.24% of reference with a coverageData >= 38X There is a 2.04% of reference with a coverageData >= 39X There is a 1.86% of reference with a coverageData >= 40X There is a 1.71% of reference with a coverageData >= 41X There is a 1.57% of reference with a coverageData >= 42X There is a 1.45% of reference with a coverageData >= 43X There is a 1.34% of reference with a coverageData >= 44X There is a 1.24% of reference with a coverageData >= 45X There is a 1.15% of reference with a coverageData >= 46X There is a 1.08% of reference with a coverageData >= 47X There is a 1.01% of reference with a coverageData >= 48X There is a 0.94% of reference with a coverageData >= 49X There is a 0.89% of reference with a coverageData >= 50X There is a 0.83% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 640495269 8.419704549399126 13.714979899306567 NC_088854.1 61469542 745233927 12.123629081212286 10.783954284727523 NC_088855.1 61039741 746406554 12.228206440128899 10.892454916672019 NC_088856.1 57946171 569816229 9.833544118040173 12.127805796752677 NC_088857.1 57274926 672324176 11.738542900954599 10.991575780438078 NC_088858.1 56905015 695048402 12.214185375401447 10.693547701986436 NC_088859.1 53672946 679584383 12.661581553581948 11.60078257386904 NC_088860.1 51133819 549740470 10.751015291856062 11.388838055209076 NC_088861.1 50364239 414269753 8.225474289406021 10.788782031711282 NC_088862.1 37310742 357494722 9.58154951729451 11.872460179326469 NW_027062568.1 15579 120222 7.716926632004622 7.216031958643248 NW_027062569.1 16498 219674 13.315189719966057 16.323982049196935 NW_027062570.1 4000 207094 51.7735 49.00705470388932 NW_027062571.1 36893 7465 0.20234190767896348 0.8890886278764663 NW_027062572.1 51000 41959 0.8227254901960784 2.334181891427564 NW_027062573.1 2000 97330 48.665 47.75461553609243 NW_027062574.1 37061 3302 0.08909635465853592 0.5179221700185259 NW_027062575.1 49428 398500 8.062231933317149 15.423628186446377 NW_027062576.1 49232 192870 3.9175739356516086 8.126702944786196 NW_027062577.1 17087 146179 8.554983320653129 6.313631053792262 NW_027062578.1 34507 574168 16.639174660213868 9.063724882665026 NW_027062579.1 64000 700211 10.940796875 10.35521444940726 NW_027062580.1 24229 167827 6.926699409798176 8.472007181828547 NW_027062581.1 5000 50171 10.0342 11.285101858645318 NW_027062582.1 18808 147052 7.818587834963846 5.766693917466129 NW_027062583.1 1000 227 0.227 0.4188925876641887 NW_027062584.1 74000 16535 0.22344594594594594 1.7294414178533788 NW_027062585.1 39334 203708 5.178929170692022 6.15284767024152 NW_027062586.1 258015 464852 1.8016471910547835 5.397636359815635