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
MC JC 257,908 Δ776 bp [crl] [crl]
RA 264,098 G→T L50L (CTC→CTA)  ykfH ← uncharacterized protein
RA 1,197,502 C→T G11R (GGA→AGA)  ymfD ← e14 prophage; putative SAM‑dependent methyltransferase
MC JC 1,299,499 Δ1,199 bp intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA 1,544,022 1 bp→AA coding (39/1389 nt) narU ← nitrate/nitrite transporter
MC JC 1,978,503 Δ776 bp insB1–insA insB1, insA
RA 2,106,741 A→T S162S (TCT→TCA)  wbbH ← O‑antigen polymerase
RA 2,173,363 Δ2 bp intergenic (‑1/+1) gatC ← / ← gatC pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA 2,679,525 G→T A1074D (GCT→GAT)  yphG ← DUF4380 domain‑containing TPR repeat protein
RA 2,817,170 C→A E112* (GAA→TAA)  yqaB ← fructose‑1‑P and 6‑phosphogluconate phosphatase
RA 3,560,455 +G intergenic (‑2/+1) glpR ← / ← glpR pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
RA 4,111,596 G→A L179L (CTG→TTG)  yiiQ ← DUF1454 family putative periplasmic protein
RA 4,296,297 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,367,616 3 bp→TCC coding (626‑628/1437 nt) aspA ← aspartate ammonia‑lyase
RA 4,604,632 C→A A186E (GCA→GAA)  bglJ → bgl operon transcriptional activator

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913_3_pae_tpiA 4484 4531 48 2 [0] [1] 3 thrC L‑threonine synthase
* * ÷ NC_000913_3_pae_tpiA 232396 232436 41 2 [1] [0] 2 yafE putative S‑adenosyl‑L‑methionine‑dependent methyltransferase
* * ÷ NC_000913_3_pae_tpiA 356455 356455 1 2 [0] [0] 2 codA cytosine/isoguanine deaminase
* * ÷ NC_000913_3_pae_tpiA 365898 365936 39 3 [1] [0] 3 lacZ beta‑D‑galactosidase
* * ÷ NC_000913_3_pae_tpiA 366319 366401 83 2 [1] [1] 3 lacZ/lacI beta‑D‑galactosidase/lactose‑inducible lac operon transcriptional repressor
* * ÷ NC_000913_3_pae_tpiA 557418 557451 34 3 [1] [1] 3 folD bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase/ 5,10‑methylene‑tetrahydrofolate cyclohydrolase
* * ÷ NC_000913_3_pae_tpiA 722929 722966 38 3 [1] [1] 2 kdpD fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein
* * ÷ NC_000913_3_pae_tpiA 855541 855558 18 2 [0] [1] 2 ldtB L,D‑transpeptidase linking Lpp to murein
* * ÷ NC_000913_3_pae_tpiA 883782 883792 11 2 [1] [0] 2 mdfA multidrug efflux system protein
* * ÷ NC_000913_3_pae_tpiA 989763 989810 48 2 [0] [0] 2 pncB nicotinate phosphoribosyltransferase
* * ÷ NC_000913_3_pae_tpiA 1090218 1090269 52 2 [1] [1] 3 pgaA biofilm adhesin polysaccharide PGA secretin; OM porin; poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein
* * ÷ NC_000913_3_pae_tpiA 1124250 1124270 21 2 [0] [1] 2 mdtH multidrug resistance efflux transporter conferring overexpression resistance to norfloxacin and enoxacin
* * ÷ NC_000913_3_pae_tpiA 1185967 1186031 65 2 [1] [1] 2 pepT peptidase T
* * ÷ NC_000913_3_pae_tpiA 1189905 1189929 25 2 [1] [1] 2 phoP response regulator in two‑component regulatory system with PhoQ
* * ÷ NC_000913_3_pae_tpiA 1227466 1227478 13 2 [0] [1] 2 [pliG] [pliG]
* * ÷ NC_000913_3_pae_tpiA 1383281 1383323 43 3 [1] [0] 2 ycjW LacI family putative transcriptional repressor
* * ÷ NC_000913_3_pae_tpiA 1438254 1438336 83 2 [1] [1] 2 pfo pyruvate‑flavodoxin oxidoreductase
* * ÷ NC_000913_3_pae_tpiA 1600793 1600855 63 2 [1] [1] 2 lsrR lsr operon transcriptional repressor
* * ÷ NC_000913_3_pae_tpiA 1665863 1665893 31 3 [1] [1] 2 clcB H(+)/Cl(‑) exchange transporter
* * ÷ NC_000913_3_pae_tpiA 1728348 1728413 66 2 [1] [1] 2 rnt RNase T; exoribonuclease T; structured DNA 3' exonuclease; RNA processing; DNA repair
* * ÷ NC_000913_3_pae_tpiA 2001007 2001042 36 2 [1] [1] 2 [fliZ] [fliZ]
* * ÷ NC_000913_3_pae_tpiA 2193407 2193487 81 3 [1] [1] 2 mrp antiporter inner membrane protein
* * ÷ NC_000913_3_pae_tpiA 2225101 2225132 32 2 [0] [1] 2 yohC Yip1 family inner membrane protein
* * ÷ NC_000913_3_pae_tpiA 2253401 2253417 17 2 [0] [1] 2 nupX nucleoside permease
* * ÷ NC_000913_3_pae_tpiA 2286487 2286514 28 2 [0] [0] 2 yejO pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system
* * ÷ NC_000913_3_pae_tpiA 2520396 2520410 15 2 [0] [1] 2 gltX glutamyl‑tRNA synthetase
* * ÷ NC_000913_3_pae_tpiA 2634062 2634171 110 2 [1] [1] 2 [guaB] [guaB]
* * ÷ NC_000913_3_pae_tpiA 2781914 2781926 13 3 [1] [0] 2 ypjA adhesin‑like autotransporter
* * ÷ NC_000913_3_pae_tpiA 2973252 2973283 32 2 [1] [0] 2 lplT lysophospholipid transporter
* * ÷ NC_000913_3_pae_tpiA 3028065 3028099 35 2 [0] [1] 3 ghxQ guanine/hypoxanthine permease, high affinity; guanine/hypoxanthine:H+ symporter
* * ÷ NC_000913_3_pae_tpiA 3088909 3088932 24 2 [0] [1] 2 galP D‑galactose transporter
* * ÷ NC_000913_3_pae_tpiA 3250688 3250714 27 3 [1] [0] 2 yqjF putative quinol oxidase subunit
* * ÷ NC_000913_3_pae_tpiA 3333897 3333973 77 2 [0] [1] 2 ispB octaprenyl diphosphate synthase
* * ÷ NC_000913_3_pae_tpiA 3344128 3344172 45 2 [0] [1] 3 lptB lipopolysaccharide export ABC transporter ATPase
* * ÷ NC_000913_3_pae_tpiA 3423744–3424230 3424532–3424238 9–789 2 [0] [1] 2 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913_3_pae_tpiA 3463997 3464068 72 2 [0] [1] 2 gspL general secretory pathway component, cryptic
* * ÷ NC_000913_3_pae_tpiA 3729226 3729278 53 2 [0] [1] 2 xylB xylulokinase
* * ÷ NC_000913_3_pae_tpiA 3907790 3907841 52 2 [1] [0] 2 pstB phosphate ABC transporter ATPase
* * ÷ NC_000913_3_pae_tpiA 4229248 4229273 26 2 [0] [1] 2 yjbB putative Na+/Pi‑cotransporter
* * ÷ NC_000913_3_pae_tpiA 4352481 4352495 15 3 [1] [0] 2 yjdJ/ghoS GNAT family putative N‑acetyltransferase/antitoxin of GhoTS toxin‑antitoxin pair; endonuclease for ghoT mRNA
* * ÷ NC_000913_3_pae_tpiA 4367628 4367681 54 5 [0] [1] 3 aspA aspartate ammonia‑lyase
* * ÷ NC_000913_3_pae_tpiA 4604129 4604159 31 3 [1] [1] 4 bglJ bgl operon transcriptional activator

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_pae_tpiA = 12078054 (0.320)8 (0.730) 8/228 0.4 71.1% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913_3_pae_tpiA = 1209602 3 (0.270)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913_3_pae_tpiA = 134356216 (1.280)4 (0.350) 4/236 1.0 20.2% intergenic (‑234/+35) osmB/yciT osmotically and stress inducible lipoprotein/global regulator of transcription; DeoR family
?NC_000913_3_pae_tpiA = 1343568 17 (1.500)intergenic (‑240/+29) osmB/yciT osmotically and stress inducible lipoprotein/global regulator of transcription; DeoR family
* ? NC_000913_3_pae_tpiA 1755687 =3 (0.240)11 (0.880) 3/260 1.4 78.6% intergenic (‑546/‑11) ydhZ/pykF uncharacterized protein/pyruvate kinase I
?NC_000913_3_pae_tpiA 2101749 = NA (NA)intergenic (‑5/+146) wbbL/insH1 pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator
* ? NC_000913_3_pae_tpiA = 17556913 (0.240)15 (1.210) 10/258 0.3 83.4% intergenic (‑550/‑7) ydhZ/pykF uncharacterized protein/pyruvate kinase I
?NC_000913_3_pae_tpiA = 2290112 NA (NA)intergenic (‑31/+2) insH1/yejO IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system
* ? NC_000913_3_pae_tpiA = 179295011 (0.880)3 (0.250) 3/246 1.3 20.4% coding (609/750 nt) btuD vitamin B12 ABC transporter ATPase
?NC_000913_3_pae_tpiA = 1792973 13 (1.100)coding (586/750 nt) btuD vitamin B12 ABC transporter ATPase
* ? NC_000913_3_pae_tpiA = 207508514 (1.120)5 (0.430) 5/244 0.9 28.5% coding (307/1533 nt) yeeR CP4‑44 prophage; putative membrane protein
?NC_000913_3_pae_tpiA = 2075092 12 (1.020)coding (314/1533 nt) yeeR CP4‑44 prophage; putative membrane protein
* ? NC_000913_3_pae_tpiA = 2146653NA (NA)3 (0.250) 3/246 1.3 NA noncoding (54/84 nt) REP147 (repetitive extragenic palindromic) element; contains 2 REP sequences REP147 (repetitive extragenic palindromic) element; contains 2 REP sequences
?NC_000913_3_pae_tpiA = 2146683 NA (NA)noncoding (84/84 nt) REP147 (repetitive extragenic palindromic) element; contains 2 REP sequences REP147 (repetitive extragenic palindromic) element; contains 2 REP sequences
* ? NC_000913_3_pae_tpiA 2177435 =NA (NA)4 (0.330) 4/250 1.1 33.3% noncoding (28/77 nt) REP151 (repetitive extragenic palindromic) element; contains 2 REP sequences REP151 (repetitive extragenic palindromic) element; contains 2 REP sequences
?NC_000913_3_pae_tpiA 2177460 = 8 (0.660)noncoding (53/77 nt) REP151 (repetitive extragenic palindromic) element; contains 2 REP sequences REP151 (repetitive extragenic palindromic) element; contains 2 REP sequences
* ? NC_000913_3_pae_tpiA = 249927612 (0.960)4 (0.340) 4/244 1.1 24.8% coding (606/1698 nt) ypdA sensor kinase regulating yhjX; pyruvate‑responsive YpdAB two‑component system
?NC_000913_3_pae_tpiA = 2499293 13 (1.110)coding (623/1698 nt) ypdA sensor kinase regulating yhjX; pyruvate‑responsive YpdAB two‑component system
* ? NC_000913_3_pae_tpiA 3559450 =10 (0.800)4 (0.330) 4/248 1.1 34.0% coding (1183/1599 nt) rtcR sigma 54‑dependent transcriptional regulator of rtcBA expression
?NC_000913_3_pae_tpiA 3559496 = 6 (0.500)coding (1229/1599 nt) rtcR sigma 54‑dependent transcriptional regulator of rtcBA expression
* ? NC_000913_3_pae_tpiA = 38705949 (0.720)6 (0.510) 6/246 0.7 42.1% coding (1137/1293 nt) dgoT D‑galactonate transporter
?NC_000913_3_pae_tpiA = 3870607 8 (0.680)coding (1124/1293 nt) dgoT D‑galactonate transporter
* ? NC_000913_3_pae_tpiA = 38761116 (0.480)3 (0.260) 3/240 1.3 30.7% intergenic (+17/+29) yidX/yidA putative lipoprotein/sugar phosphate phosphatase
?NC_000913_3_pae_tpiA = 3876122 8 (0.690)intergenic (+28/+18) yidX/yidA putative lipoprotein/sugar phosphate phosphatase
* ? NC_000913_3_pae_tpiA = 415032912 (0.960)6 (0.510) 6/242 0.7 36.2% intergenic (‑148/+34) eptC/ppc LPS heptose I phosphoethanolamine transferase/phosphoenolpyruvate carboxylase
?NC_000913_3_pae_tpiA = 4150339 10 (0.860)intergenic (‑158/+24) eptC/ppc LPS heptose I phosphoethanolamine transferase/phosphoenolpyruvate carboxylase
* ? NC_000913_3_pae_tpiA 4201698 =8 (0.640)3 (0.280) 3/226 1.2 31.7% intergenic (‑94/‑144) zraP/zraS Zn‑dependent periplasmic chaperone/sensory histidine kinase in two‑component regulatory system with ZraR
?NC_000913_3_pae_tpiA 4201744 = 6 (0.550)intergenic (‑140/‑98) zraP/zraS Zn‑dependent periplasmic chaperone/sensory histidine kinase in two‑component regulatory system with ZraR
* ? NC_000913_3_pae_tpiA = 450202017 (1.360)4 (0.350) 4/238 1.1 20.8% coding (1328/1329 nt) insG IS4 transposase
?NC_000913_3_pae_tpiA = 4502024 15 (1.310)coding (1324/1329 nt) insG IS4 transposase
* ? NC_000913_3_pae_tpiA 4527689 =4 (0.320)6 (0.510) 6/244 0.7 64.0% coding (208/432 nt) sgcA putative phosphotransferase enzyme IIA component
?NC_000913_3_pae_tpiA 4527721 = 3 (0.260)coding (176/432 nt) sgcA putative phosphotransferase enzyme IIA component
* ? NC_000913_3_pae_tpiA 4542598 =8 (0.640)3 (0.260) 3/242 1.3 21.9% intergenic (+49/‑433) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913_3_pae_tpiA 4542912 = 14 (1.200)intergenic (+363/‑119) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)