breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
RA 49,765 C→T intergenic (+134/‑58) kefC → / → folA glutathione‑regulated potassium‑efflux system protein KefC/type 3 dihydrofolate reductase
RA 49,884 C→A P21Q (CCG→CAG)  folA → type 3 dihydrofolate reductase
MC JC 1,613,631 Δ3 bp coding (255‑257/435 nt) marR → multiple antibiotic resistance transcriptional regulator MarR
RA 2,236,503 G→A T210M (ACG→ATG)  folE ← GTP cyclohydrolase I FolE
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA
RA 3,632,461 T→G L487R (CTT→CGT)  pitA → inorganic phosphate transporter PitA
RA 3,754,231 G→T R127S (CGC→AGC)  selA ← L‑seryl‑tRNA(Sec) selenium transferase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 255922 255967 46 3 [1] [1] 2 phoE/proB phosphoporin PhoE/glutamate 5‑kinase
* * ÷ NZ_CP009273 356981 357578 598 2 [0] [1] 2 [lacA] [lacA]
* * ÷ NZ_CP009273 380412 380420 9 2 [0] [1] 3 BW25113_RS01880/tauA PIG‑L family deacetylase/taurine ABC transporter substrate‑binding protein
* * ÷ NZ_CP009273 632184 632238 55 2 [1] [1] 2 ybdO LysR family transcriptional regulator
* * ÷ NZ_CP009273 703451 703540 90 5 [1] [1] 2 glnS/chiP glutamine‑‑tRNA ligase/chitoporin
* * ÷ NZ_CP009273 729236 729266 31 2 [1] [0] 4 BW25113_RS03630 hypothetical protein
* * ÷ NZ_CP009273 982718 982728 11 2 [0] [1] 2 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 1051176 1051188 13 2 [0] [0] 2 torS TMAO reductase system sensor histidine kinase/response regulator TorS
* * ÷ NZ_CP009273 1158327 1158352 26 2 [1] [1] 3 lpoB penicillin‑binding protein activator LpoB
* * ÷ NZ_CP009273 1207066 1207129 64 2 [1] [1] 3 BW25113_RS23640/iraM isocitrate/isopropylmalate family dehydrogenase/anti‑adapter protein IraM
* * ÷ NZ_CP009273 1229286 1229315 30 2 [1] [0] 2 nhaB Na(+)/H(+) antiporter NhaB
* * ÷ NZ_CP009273 1281532 1281551 20 2 [0] [1] 2 narI respiratory nitrate reductase subunit gamma
* * ÷ NZ_CP009273 1305425 1305430 6 2 [0] [0] 4 tonB TonB system transport protein TonB
* * ÷ NZ_CP009273 1427977–1428258 1428279 22–303 3 [1] [1] 2 [ydfK] [ydfK]
* * ÷ NZ_CP009273 1524310 1524427 118 2 [0] [1] 4 [BW25113_RS26145] [BW25113_RS26145]
* * ÷ NZ_CP009273 1594169 1594169 1 4 [0] [0] 5 lsrK autoinducer‑2 kinase
* * ÷ NZ_CP009273 1617039 1617044 6 3 [0] [1] 2 mgtT protein MgtT
* * ÷ NZ_CP009273 1646931 1646952 22 2 [1] [1] 2 BW25113_RS25635 tyrosine‑type recombinase/integrase
* * ÷ NZ_CP009273 1748938 1748976 39 2 [1] [1] 2 ydhY/fumD ferredoxin‑like protein/fumarate hydratase FumD
* * ÷ NZ_CP009273 1757738 1757743 6 2 [1] [1] 2 sufB Fe‑S cluster assembly protein SufB
* * ÷ NZ_CP009273 1864569 1864630 62 2 [1] [1] 2 yeaH/cdgI YeaH/YhbH family protein/GGDEF domain‑containing protein
* * ÷ NZ_CP009273 1940855 1940925 71 2 [1] [1] 2 yebB YebB family permuted papain‑like enzyme
* * ÷ NZ_CP009273 1946078 1946121 44 3 [1] [1] 2 yecE DUF72 domain‑containing protein
* * ÷ NZ_CP009273 2024381 2024404 24 2 [1] [1] 4 dcm DNA‑cytosine methyltransferase
* * ÷ NZ_CP009273 2027032 2027124 93 2 [1] [1] 2 drpB/ompC cell division protein DrpB/porin OmpC
* * ÷ NZ_CP009273 2050102 2050191 90 3 [1] [1] 2 amn/yeeN AMP nucleosidase/YebC/PmpR family DNA‑binding transcriptional regulator
* * ÷ NZ_CP009273 2051100 2051153 54 2 [0] [0] 4 yeeN/BW25113_RS10360 YebC/PmpR family DNA‑binding transcriptional regulator/tRNA‑Asn
* * ÷ NZ_CP009273 2097466 2097517 52 2 [1] [1] 3 wbbK glycosyltransferase family 1 protein
* * ÷ NZ_CP009273 2100158 2100210 53 3 [1] [1] 2 wzy O16 family O‑antigen polymerase
* * ÷ NZ_CP009273 2101611 2101661 51 2 [1] [1] 2 glf UDP‑galactopyranose mutase
* * ÷ NZ_CP009273 2170672 2170694 23 2 [0] [1] 3 [gatY] [gatY]
* * ÷ NZ_CP009273 2185806 2185840 35 2 [0] [1] 2 yehD/yehE fimbrial protein/YehE family protein
* * ÷ NZ_CP009273 2357920 2357965 46 2 [1] [1] 2 yfaZ/nudI YfaZ family protein/nucleoside triphosphatase NudI
* * ÷ NZ_CP009273 2463684 2463768 85 5 [1] [0] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2463844 2463868 25 2 [0] [1] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2768270 2768299 30 2 [1] [1] 2 BW25113_RS13770 hypothetical protein
* * ÷ NZ_CP009273 2897122 2897184 63 2 [1] [1] 2 ygcE/queE FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE
* * ÷ NZ_CP009273 2988549 2988597 49 2 [1] [1] 2 BW25113_RS14850/BW25113_RS26010 response regulator transcription factor/hypothetical protein
* * ÷ NZ_CP009273 3178654 3178735 82 2 [1] [1] 2 ubiK/ygiL ubiquinone biosynthesis accessory factor UbiK/fimbrial‑like protein
* * ÷ NZ_CP009273 3463354 3463400 47 2 [1] [1] 2 chiA/tuf bifunctional chitinase/lysozyme/elongation factor Tu
* * ÷ NZ_CP009273 3576003 3576006 4 4 [0] [0] 2 hcp Hcp1 family type VI secretion system effector
* * ÷ NZ_CP009273 3792637 3792686 50 2 [1] [1] 2 [waaU] [waaU]
* * ÷ NZ_CP009273 4258769 4258825 57 2 [1] [1] 2 BW25113_RS26020 hypothetical protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 269666 =NA (NA)19 (0.930) 8/166 0.8 100% intergenic (+2/+146) ykfC/BW25113_RS01325 reverse transcriptase domain‑containing protein/IS5‑like element IS5 family transposase
?NZ_CP009273 = 481436 0 (0.000)coding (220/648 nt) acrR multidrug efflux transporter transcriptional repressor AcrR
* ? NZ_CP009273 360104 =NA (NA)49 (2.390) 28/166 0.0 NA intergenic (‑35/+251) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
?NZ_CP009273 = 360286 NA (NA)intergenic (‑217/+69) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
* ? NZ_CP009273 481433 =0 (0.000)26 (1.270) 19/166 0.1 100% coding (217/648 nt) acrR multidrug efflux transporter transcriptional repressor AcrR
?NZ_CP009273 = 571241 NA (NA)coding (1041/1068 nt) BW25113_RS02855 porin
* ? NZ_CP009273 1203246 =2 (0.100)11 (0.670) 10/134 0.4 85.9% coding (290/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 1205075 = 2 (0.120)coding (40/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 12032612 (0.100)5 (0.300) 3/134 1.4 73.5% coding (305/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 = 1205058 2 (0.120)coding (57/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 1391494NA (NA)12 (0.590) 8/164 0.7 100% intergenic (+145/‑128) BW25113_RS06980/ynaJ IS5‑like element IS5 family transposase/DUF2534 family protein
?NZ_CP009273 1972747 = 0 (0.000)intergenic (‑293/‑487) flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
* ? NZ_CP009273 = 19727510 (0.000)24 (1.170) 18/166 0.2 100% intergenic (‑297/‑483) flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
?NZ_CP009273 = 2283592 NA (NA)intergenic (‑68/‑387) BW25113_RS11435/narP IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP
* ? NZ_CP009273 4532499 =3 (0.150)13 (0.710) 9/148 0.5 77.2% intergenic (+49/‑433) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 4532813 = 5 (0.270)intergenic (+363/‑119) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA