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

Predicted mutations
evidence position mutation freq annotation gene description
RA 169,015 G→A 68.4% W511* (TGG→TAG)  fhuA → ferrichrome outer membrane transporter
RA 169,034 C→A 17.7% Y517* (TAC→TAA fhuA → ferrichrome outer membrane transporter
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 268,865 T→A 5.3% L32F (TTA→TTT ykfA ← CP4‑6 prophage; putative GTP‑binding protein
RA 282,428 G→A 5.3% G51S (GGC→AGC)  yagE → 2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage
RA 356,794 C→T 5.7% Y208Y (TAC→TAT codA → cytosine/isoguanine deaminase
RA 656,862 G→A 5.2% S102S (TCG→TCA pagP → phospholipid:lipid A palmitoyltransferase
RA 662,683 A→T 5.5% intergenic (‑41/+69) ybeD ← / ← dacA UPF0250 family protein/D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 5)
RA 662,684 G→T 5.8% intergenic (‑42/+68) ybeD ← / ← dacA UPF0250 family protein/D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 5)
RA 662,685 A→C 5.3% intergenic (‑43/+67) ybeD ← / ← dacA UPF0250 family protein/D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 5)
RA 662,686 A→T 5.3% intergenic (‑44/+66) ybeD ← / ← dacA UPF0250 family protein/D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 5)
RA 764,445 G→A 5.1% G89D (GGC→GAC)  sucD → succinyl‑CoA synthetase, NAD(P)‑binding, alpha subunit
RA 777,363 C→T 6.2% A341V (GCC→GTC)  tolA → membrane anchored protein in TolA‑TolQ‑TolR complex
RA 875,393 C→A 8.6% S20* (TCA→TAA)  yliF → putative membrane‑anchored diguanylate cyclase
RA 987,560 G→C 5.1% intergenic (‑578/+25) ompF ← / ← asnS outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
RA 1,082,418 A→T 5.2% N59I (AAC→ATC)  efeO → inactive ferrous ion transporter EfeUOB
RA 1,128,454 Δ1 bp 5.2% coding (616/1536 nt) murJ → putative lipid II flippase
MC JC 1,299,499 Δ1,199 bp 100% intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA 1,316,235 G→T 5.1% intergenic (‑200/+181) yciG ← / ← trpA KGG family protein/tryptophan synthase, alpha subunit
RA 1,371,933 T→A 5.2% L9I (TTA→ATA)  ycjN → putative ABC sugar transporter periplasmic binding protein
RA 1,410,986 A→G 5.7% intergenic (+102/+27) dbpA → / ← ttcA ATP‑dependent RNA helicase, specific for 23S rRNA/tRNA s(2)C32 thioltransferase, iron sulfur cluster protein
RA 1,458,783 C→T 5.4% Q174* (CAG→TAG)  paaG → 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming
RA 1,490,226 T→C 6.9% pseudogene (488/750 nt) gapC ← pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment)
RA 1,510,710 G→A 5.9% Q236Q (CAG→CAA ydcR → putative DNA‑binding transcriptional regulator and putative aminotransferase
RA 1,614,396 T→C 6.9% H103R (CAT→CGT)  sad ← succinate semialdehyde dehydrogenase, NAD(P)+‑dependent
RA 1,615,422 G→A 6.4% A207T (GCC→ACC)  yneJ → putative DNA‑binding transcriptional regulator
RA 1,647,434 A→T 5.1% pseudogene (203/279 nt) ydfX ← pseudogene, Qin prophage;Phage or Prophage Related
RA 1,660,200 C→G 5.6% A711G (GCC→GGC)  ynfE → putative selenate reductase, periplasmic
RA 1,662,350 C→T 100% P599S (CCC→TCC)  ynfF → S‑ and N‑oxide reductase, A subunit, periplasmic
RA 1,671,938 T→C 5.1% intergenic (+78/‑22) ydgU → / → ydgD stationary phase‑induced protein/putative peptidase
RA 1,689,817 C→A 5.2% intergenic (+66/‑35) manA → / → ydgA mannose‑6‑phosphate isomerase/DUF945 family protein
RA 1,689,819 A→T 6.1% intergenic (+68/‑33) manA → / → ydgA mannose‑6‑phosphate isomerase/DUF945 family protein
RA 1,689,821 T→G 5.5% intergenic (+70/‑31) manA → / → ydgA mannose‑6‑phosphate isomerase/DUF945 family protein
RA 1,708,662 C→G 12.0% Q582E (CAA→GAA)  rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,708,958 T→C 20.4% V680V (GTT→GTC rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,744,575 T→C 5.3% I373I (ATT→ATC mdtK → multidrug efflux system transporter
RA 1,764,687 T→C 5.7% intergenic (‑301/+26) sufA ← / ← rydB Fe‑S cluster assembly protein/novel sRNA, function unknown
RA 1,769,727 Δ1 bp 5.5% coding (654/1113 nt) ydiK → UPF0118 family inner membrane protein
RA 1,799,167 A→C 5.2% intergenic (‑225/+59) pheS ← / ← pheM phenylalanine tRNA synthetase, alpha subunit/phenylalanyl‑tRNA synthetase operon leader peptide
RA 1,805,405 T→C 5.3% T227A (ACA→GCA)  ydiY ← acid‑inducible putative outer membrane protein
RA 1,806,335 G→T 100% intergenic (‑252/‑35) ydiY ← / → pfkB acid‑inducible putative outer membrane protein/6‑phosphofructokinase II
RA 1,840,330 A→G 6.3% A288A (GCA→GCG ynjE → molybdopterin synthase sulfurtransferase
RA 1,965,190 T→C 7.4% Q334Q (CAA→CAG flhB ← flagellin export apparatus, substrate specificity protein
RA 1,965,904 A→G 5.4% I96I (ATT→ATC flhB ← flagellin export apparatus, substrate specificity protein
RA 1,965,907 C→T 5.2% L95L (CTG→CTA flhB ← flagellin export apparatus, substrate specificity protein
MC JC 1,978,503 Δ776 bp 100% insB1insA insB1, insA
RA 1,980,240 C→A 5.5% S458I (AGC→ATC) ‡ otsA ← trehalose‑6‑phosphate synthase
RA 1,980,241 T→A 5.6% S458C (AGC→TGC) ‡ otsA ← trehalose‑6‑phosphate synthase
RA 1,980,242 T→G 6.3% R457R (CGA→CGC otsA ← trehalose‑6‑phosphate synthase
RA 1,983,452 A→T 5.9% V30E (GTG→GAG)  araH ← L‑arabinose ABC transporter permease
RA 2,059,939 G→T 6.3% intergenic (+13/+25) asnU → / ← cbl tRNA‑Asn/ssuEADCB/tauABCD operon transcriptional activator
RA 2,059,946 T→A 5.3% intergenic (+20/+18) asnU → / ← cbl tRNA‑Asn/ssuEADCB/tauABCD operon transcriptional activator
RA 2,059,948 T→A 5.3% intergenic (+22/+16) asnU → / ← cbl tRNA‑Asn/ssuEADCB/tauABCD operon transcriptional activator
RA 2,091,487 A→G 5.7% I131V (ATT→GTT)  hisD → bifunctional histidinal dehydrogenase/ histidinol dehydrogenase
RA 2,173,361 Δ2 bp 100% pseudogene (1‑2/442 nt) gatC ← pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA 2,181,691 T→C 5.5% V199A (GTG→GCG)  yegV → putative kinase
RA 2,229,278 G→A 7.7% intergenic (+213/+160) yohP → / ← dusC uncharacterized protein/tRNA‑dihydrouridine synthase C
RA 2,274,192 T→C 7.0% L5P (CTG→CCG)  yejB → microcin C ABC transporter permease
RA 2,304,988 T→C 5.7% intergenic (+595/+120) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,305,085 A→G 7.9% intergenic (+692/+23) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,305,086 C→G 7.9% intergenic (+693/+22) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,305,087 C→T 7.9% intergenic (+694/+21) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,318,922 C→T 5.2% A319T (GCA→ACA)  rcsC ← hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA 2,519,222 T→G 6.1% intergenic (+17/+35) yfeD → / ← gltX DUF1323 family putative DNA‑binding protein/glutamyl‑tRNA synthetase
RA 2,519,225 T→A 6.1% intergenic (+20/+32) yfeD → / ← gltX DUF1323 family putative DNA‑binding protein/glutamyl‑tRNA synthetase
RA 2,519,228 C→A 6.5% intergenic (+23/+29) yfeD → / ← gltX DUF1323 family putative DNA‑binding protein/glutamyl‑tRNA synthetase
RA 2,525,312 T→A 5.0% G62G (GGT→GGA yfeN → putative outer membrane protein
RA 2,560,996 G→T 27.0% intergenic (+98/‑372) yffL → / → yffM CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA 2,616,840 G→A 5.1% P249P (CCG→CCA bepA → OM protein maintenance and assembly metalloprotease and chaperone, periplasmic
RA 2,653,367 G→A 6.1% intergenic (+28/‑488) sseA → / → ryfA 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown
RA 2,653,372 T→C 6.6% intergenic (+33/‑483) sseA → / → ryfA 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown
RA 2,660,199 T→C 5.4% M31V (ATG→GTG)  iscU ← iron‑sulfur cluster assembly scaffold protein
RA 2,677,405 A→T 6.1% I319I (ATT→ATA yphE ← putative sugar ABC transporter ATPase
RA 2,691,169 A→T 5.9% noncoding (172/184 nt) glmY ← sRNA activator of glmS mRNA, glmZ processing antagonist
RA 2,691,171 T→A 6.0% noncoding (170/184 nt) glmY ← sRNA activator of glmS mRNA, glmZ processing antagonist
RA 2,691,173 A→T 6.0% noncoding (168/184 nt) glmY ← sRNA activator of glmS mRNA, glmZ processing antagonist
RA 2,699,290 T→C 5.1% S178P (TCC→CCC)  yfhH → putative DNA‑binding transcriptional regulator
RA 2,789,148 A→T 5.5% Q55L (CAG→CTG)  csiD → carbon starvation protein
RA 2,877,871 A→T 6.7% intergenic (+253/+698) iap → / ← ygbF aminopeptidase in alkaline phosphatase isozyme conversion/CRISPR adaptation ssRNA endonuclease
RA 3,034,756 C→T 5.2% C140Y (TGC→TAC)  lysS ← lysine tRNA synthetase, constitutive
RA 3,074,559 G→A 6.4% T44M (ACG→ATG)  yggC ← putative PanK family P‑loop kinase
RA 3,154,920 G→A 5.4% P100L (CCG→CTG)  yqhC ← transcriptional activator of yqhD
RA 3,161,358 G→C 5.1% Q438E (CAG→GAG)  ftsP ← septal ring component that protects the divisome from stress; multicopy suppressor of ftsI(Ts)
RA 3,243,989 T→C 5.0% E251E (GAA→GAG uxaC ← uronate isomerase
RA 3,269,956 T→C 7.4% intergenic (+354/+260) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
JC 3,406,399 Δ3 bp 6.3% coding (483‑485/1350 nt) accC → acetyl‑CoA carboxylase, biotin carboxylase subunit
RA 3,514,021 C→T 5.3% L123L (TTG→TTA gph ← phosphoglycolate phosphatase
RA 3,523,857 G→T 5.6% S329S (TCG→TCT mrcA → penicillin‑binding protein 1a, murein transglycosylase and transpeptidase
RA 3,560,455:1 +G 100% 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 3,601,507 G→T 5.1% R194S (CGT→AGT)  ftsX ← putative ABC transporter permease
RA 3,613,431 A→G 5.8% S155G (AGC→GGC)  acpT → 4'‑phosphopantetheinyl transferase
RA 3,692,807 T→A 5.6% E810D (GAA→GAT bcsA ← cellulose synthase, catalytic subunit
RA 3,728,215 T→A 5.9% K386I (AAA→ATA)  xylB ← xylulokinase
RA 3,760,782 C→T 5.4% A156A (GCG→GCA selA ← selenocysteine synthase
RA 3,815,801 Δ1 bp 100% intergenic (‑33/+33) pyrE ← / ← rph orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
RA 4,137,909 A→C 5.5% intergenic (‑252/+23) yijF ← / ← gldA DUF1287 family protein/glycerol dehydrogenase, NAD+ dependent; 1,2‑propanediol:NAD+ oxidoreductase
RA 4,137,910 C→T 5.5% intergenic (‑253/+22) yijF ← / ← gldA DUF1287 family protein/glycerol dehydrogenase, NAD+ dependent; 1,2‑propanediol:NAD+ oxidoreductase
RA 4,137,911 A→T 5.4% intergenic (‑254/+21) yijF ← / ← gldA DUF1287 family protein/glycerol dehydrogenase, NAD+ dependent; 1,2‑propanediol:NAD+ oxidoreductase
RA 4,137,912 A→G 5.5% intergenic (‑255/+20) yijF ← / ← gldA DUF1287 family protein/glycerol dehydrogenase, NAD+ dependent; 1,2‑propanediol:NAD+ oxidoreductase
RA 4,183,106 C→T 100% S621F (TCC→TTC)  rpoB → RNA polymerase, beta subunit
RA 4,296,060 C→T 38.1% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,380:1 +CG 100% intergenic (+586/+56) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,392,506 C→G 10.6% noncoding (35/76 nt) glyX → tRNA‑Gly
RA 4,421,967 A→G 5.1% K87R (AAG→AGG)  ulaC → L‑ascorbate‑specific enzyme IIA component of PTS
RA 4,451,714 C→T 5.4% R219R (CGC→CGT ytfR → putative sugar ABC transporter ATPase
RA 4,456,659 G→A 5.2% R292H (CGC→CAC)  mpl → UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase
RA 4,521,083 A→G 5.2% L313P (CTG→CCG)  yjhF ← putative transporter
RA 4,521,385 G→T 5.4% A212A (GCC→GCA yjhF ← putative transporter
RA 4,597,121 C→T 5.7% intergenic (+109/+29) lgoD → / ← opgB L‑galactonate oxidoreductase; L‑gulonate oxidoreductase/OPG periplasmic biosynthetic phosphoglycerol transferases I (membrane‑bound) and II (soluble)
RA 4,597,122 C→A 5.7% intergenic (+110/+28) lgoD → / ← opgB L‑galactonate oxidoreductase; L‑gulonate oxidoreductase/OPG periplasmic biosynthetic phosphoglycerol transferases I (membrane‑bound) and II (soluble)
RA 4,597,123 C→G 5.5% intergenic (+111/+27) lgoD → / ← opgB L‑galactonate oxidoreductase; L‑gulonate oxidoreductase/OPG periplasmic biosynthetic phosphoglycerol transferases I (membrane‑bound) and II (soluble)
RA 4,597,125 A→G 5.3% intergenic (+113/+25) lgoD → / ← opgB L‑galactonate oxidoreductase; L‑gulonate oxidoreductase/OPG periplasmic biosynthetic phosphoglycerol transferases I (membrane‑bound) and II (soluble)
RA 4,606,239 A→G 14.0% noncoding (48/87 nt) leuP ← tRNA‑Leu

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 3423772–3424234 3424561–3424238 5–790 34 [33] [33] 35 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 4107545 4108516 972 34 [31] [33] 35 pfkA pfkA
* * ÷ NC_000913 4144017 4147128 3112 34 [33] [33] 34 [pflD]–[pflC] [pflD],[pflC]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 16653NA (NA)4 (0.050) 4/244 NT NA noncoding (1267/1345 nt) IS186 repeat region
?NC_000913 = 16691 NA (NA)noncoding (1305/1345 nt) IS186 repeat region
* ? NC_000913 = 274347NA (NA)4 (0.050) 4/250 NT NA noncoding (803/1195 nt) IS5 repeat region
?NC_000913 = 274354 NA (NA)noncoding (796/1195 nt) IS5 repeat region
* ? NC_000913 274620 =NA (NA)4 (0.050) 4/240 NT NA noncoding (530/1195 nt) IS5 repeat region
?NC_000913 274663 = NA (NA)noncoding (487/1195 nt) IS5 repeat region
* ? NC_000913 = 381669NA (NA)3 (0.040) 3/244 NT NA noncoding (410/1331 nt) IS2 repeat region
?NC_000913 = 381695 NA (NA)noncoding (436/1331 nt) IS2 repeat region
* ? NC_000913 1063031 =82 (0.940)6 (0.070) 6/252 NT 7.1% coding (745/921 nt) cbpA DnaK co‑chaperone; curved DNA‑binding protein
?NC_000913 1063051 = 78 (0.920)coding (725/921 nt) cbpA DnaK co‑chaperone; curved DNA‑binding protein
* ? NC_000913 1207790 =30 (0.340)19 (0.250) 19/226 NT 33.6% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 49 (0.640)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780529 (0.330)16 (0.210) 15/226 NT 30.1% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 49 (0.640)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 1366959 =62 (0.710)4 (0.050) 4/244 NT 6.3% coding (954/978 nt) pspF psp operon transcriptional activator
?NC_000913 1367004 = 61 (0.740)coding (909/978 nt) pspF psp operon transcriptional activator
* ? NC_000913 = 182593593 (1.070)5 (0.060) 5/236 NT 5.3% intergenic (‑310/+20) spy/astE periplasmic ATP‑independent protein refolding chaperone, stress‑induced/succinylglutamate desuccinylase
?NC_000913 = 1825939 94 (1.180)intergenic (‑314/+16) spy/astE periplasmic ATP‑independent protein refolding chaperone, stress‑induced/succinylglutamate desuccinylase
* ? NC_000913 = 184174050 (0.570)4 (0.050) 4/246 NT 7.0% coding (251/408 nt) nudG CTP pyrophosphohydrolase; also hydrolyzes 2‑hydroxy‑dATP, 8‑hydroxy‑dGTP, 5‑hydroxy‑CTP, dCTP and 5‑methyl‑dCTP
?NC_000913 = 1841768 58 (0.700)coding (279/408 nt) nudG CTP pyrophosphohydrolase; also hydrolyzes 2‑hydroxy‑dATP, 8‑hydroxy‑dGTP, 5‑hydroxy‑CTP, dCTP and 5‑methyl‑dCTP
* ? NC_000913 = 2866486NA (NA)6 (0.080) 6/232 NT NA noncoding (8/18 nt) REP199 (repetitive extragenic palindromic) element; contains 1 REP sequences REP199 (repetitive extragenic palindromic) element; contains 1 REP sequences
?NC_000913 = 2866488 NA (NA)noncoding (10/18 nt) REP199 (repetitive extragenic palindromic) element; contains 1 REP sequences REP199 (repetitive extragenic palindromic) element; contains 1 REP sequences
* ? NC_000913 = 329960870 (0.800)5 (0.060) 5/238 NT 6.9% coding (308/444 nt) yhbP UPF0306 family protein
?NC_000913 = 3299630 70 (0.870)coding (286/444 nt) yhbP UPF0306 family protein
* ? NC_000913 = 3620116NA (NA)3 (0.040) 3/246 NT 100% coding (925/4236 nt) rhsB Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
?NC_000913 = 3620152 0 (0.000)coding (961/4236 nt) rhsB Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
* ? NC_000913 = 4171761116 (1.330)10 (0.120)
+TAG
4/252 NT 7.7% intergenic (+5/‑296) rrfB/murB 5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding
?NC_000913 = 4213198 131 (1.500)intergenic (+39/‑36) rrfE/yjaA 5S ribosomal RNA of rrnE operon/stress‑induced protein
* ? NC_000913 = 4603858105 (1.210)6 (0.070) 6/246 NT 5.4% coding (382/726 nt) yjjQ putative transcriptional regulator
?NC_000913 = 4603865 112 (1.350)coding (389/726 nt) yjjQ putative transcriptional regulator
* ? NC_000913 4607519 =80 (0.920)6 (0.070) 6/252 NT 7.3% coding (182/1032 nt) rsmC 16S rRNA m(2)G1207 methyltransferase, SAM‑dependent
?NC_000913 4607556 = 74 (0.870)coding (145/1032 nt) rsmC 16S rRNA m(2)G1207 methyltransferase, SAM‑dependent