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 49,898 G→A A26T (GCC→ACC)  folA → type 3 dihydrofolate reductase
RA 49,910 T→G W30G (TGG→GGG)  folA → type 3 dihydrofolate reductase
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 356981 357567 587 11 [0] [0] 2 lacA galactoside O‑acetyltransferase
* * ÷ NZ_CP009273 380369 380389 21 2 [0] [0] 2 BW25113_RS01880/tauA PIG‑L family deacetylase/taurine ABC transporter substrate‑binding protein
* * ÷ NZ_CP009273 578986 579017 32 2 [0] [0] 2 BW25113_RS26085/appY tail fiber assembly protein/DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 651715 651732 18 2 [1] [1] 3 dcuC/pagP anaerobic C4‑dicarboxylate transporter DcuC/lipid IV(A) palmitoyltransferase PagP
* * ÷ NZ_CP009273 716396 716436 41 3 [1] [0] 4 BW25113_RS26090/kdpE leader peptide SpeFL/two‑component system response regulator KdpE
* * ÷ NZ_CP009273 766297 766353 57 2 [1] [1] 2 mngB/cydA mannosylglycerate hydrolase/cytochrome ubiquinol oxidase subunit I
* * ÷ NZ_CP009273 982718 982728 11 3 [0] [0] 5 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 993098 993107 10 4 [0] [0] 2 ssuE/elfA NADPH‑dependent FMN reductase/fimbrial protein
* * ÷ NZ_CP009273 993889 993914 26 2 [0] [1] 5 elfA/elfD fimbrial protein/molecular chaperone
* * ÷ NZ_CP009273 1098624 1098632 9 2 [0] [1] 3 csgD biofilm master transcriptional regulator CsgD
* * ÷ NZ_CP009273 1192704 1192714 11 3 [0] [1] 2 ymfD class I SAM‑dependent methyltransferase
* * ÷ NZ_CP009273 1193247 1193279 33 3 [1] [1] 2 BW25113_RS05920 hypothetical protein
* * ÷ NZ_CP009273 1193517 1193541 25 2 [0] [0] 2 BW25113_RS05920 hypothetical protein
* * ÷ NZ_CP009273 1212066 1212121 56 2 [0] [1] 3 [ariR] [ariR]
* * ÷ NZ_CP009273 1215785 1215804 20 3 [0] [0] 4 BW25113_RS25990 autotransporter outer membrane beta‑barrel domain‑containing protein
* * ÷ NZ_CP009273 1389983 1390012 30 2 [1] [1] 4 ynaI low conductance mechanosensitive channel YnaI
* * ÷ NZ_CP009273 1459449 1459516 68 2 [1] [1] 2 [BW25113_RS25580] [BW25113_RS25580]
* * ÷ NZ_CP009273 1521302 1521332 31 2 [0] [1] 4 yncH YncH family protein
* * ÷ NZ_CP009273 1539082 1539082 1 2 [0] [0] 2 BW25113_RS07710 leucine‑rich repeat domain‑containing protein
* * ÷ NZ_CP009273 1539476 1539509 34 3 [1] [1] 2 BW25113_RS07710 leucine‑rich repeat domain‑containing protein
* * ÷ NZ_CP009273 1631762 1631762 1 2 [0] [0] 2 ydfO/gnsB DUF1398 domain‑containing protein/addiction module toxin, GnsA/GnsB family
* * ÷ NZ_CP009273 1635012 1635032 21 2 [0] [1] 2 essD/ynfU phage lysis protein EssD/putative zinc‑binding protein YnfU
* * ÷ NZ_CP009273 1783823 1783859 37 2 [1] [1] 2 aroH/hemP 3‑deoxy‑7‑phosphoheptulonate synthase AroH/hemin uptake protein HemP
* * ÷ NZ_CP009273 1797615 1797667 53 2 [1] [1] 4 espL1 type III secretion system effector EspL1
* * ÷ NZ_CP009273 2027309 2027321 13 3 [0] [0] 2 drpB/ompC cell division protein DrpB/porin OmpC
* * ÷ NZ_CP009273 2050181 2050258 78 2 [0] [1] 2 amn/yeeN AMP nucleosidase/YebC/PmpR family DNA‑binding transcriptional regulator
* * ÷ NZ_CP009273 2098708 2098732 25 5 [1] [0] 2 wbbI beta‑1,6‑galactofuranosyltransferase
* * ÷ NZ_CP009273 2101634 2101651 18 2 [1] [0] 2 glf UDP‑galactopyranose mutase
* * ÷ NZ_CP009273 2185829 2185901 73 2 [0] [1] 2 yehD/yehE fimbrial protein/YehE family protein
* * ÷ NZ_CP009273 2463798 2463839 42 2 [1] [0] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2569339 2569349 11 2 [1] [0] 3 eutS/maeB ethanolamine utilization microcompartment protein EutS/NADP‑dependent oxaloacetate‑decarboxylating malate dehydrogenase
* * ÷ NZ_CP009273 2779644 2779670 27 2 [0] [1] 2 BW25113_RS13825/BW25113_RS26005 tRNA‑Ile/alpha‑amylase family glycosyl hydrolase
* * ÷ NZ_CP009273 2781142 2781142 1 5 [0] [0] 3 BW25113_RS26005 alpha‑amylase family glycosyl hydrolase
* * ÷ NZ_CP009273 2782042 2782065 24 4 [1] [0] 2 BW25113_RS26005/csiD alpha‑amylase family glycosyl hydrolase/glutarate dioxygenase GlaH
* * ÷ NZ_CP009273 2877604 2877607 4 2 [0] [0] 2 casA/cas3 type I‑E CRISPR‑associated protein Cse1/CasA/CRISPR‑associated helicase/endonuclease Cas3
* * ÷ NZ_CP009273 2877759 2877791 33 2 [1] [1] 3 casA/cas3 type I‑E CRISPR‑associated protein Cse1/CasA/CRISPR‑associated helicase/endonuclease Cas3
* * ÷ NZ_CP009273 3492786 3492794 9 2 [0] [0] 2 cysG/yhfL siroheme synthase CysG/YhfL family protein
* * ÷ NZ_CP009273 3763096 3763128 33 2 [1] [1] 3 BW25113_RS26240 Imm57 family immunity protein
* * ÷ NZ_CP009273 4258927 4258938 12 2 [0] [1] 3 BW25113_RS26020 hypothetical protein
* * ÷ NZ_CP009273 4561743 4561802 60 10 [1] [1] 2 yjiS/yjiT DUF1127 domain‑containing protein/protein YjiT

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 = 270581NA (NA)3 (0.100) 3/150 2.2 NA coding (212/981 nt) BW25113_RS01325 IS5‑like element IS5 family transposase
?NZ_CP009273 = 270584 NA (NA)coding (209/981 nt) BW25113_RS01325 IS5‑like element IS5 family transposase
* ? NZ_CP009273 360104 =NA (NA)93 (3.010) 40/156 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 1203246 =29 (0.940)5 (0.200) 5/124 1.4 25.0% coding (290/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 1205075 = 7 (0.280)coding (40/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 1391494NA (NA)11 (0.360) 7/154 1.4 100% 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)26 (0.840) 17/156 0.4 100% 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