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 12,484 C→A 20.3% Q108K (CAG→AAG)  dnaK → chaperone Hsp70, with co‑chaperone DnaJ
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 351,510 T→C 26.3% L99P (CTC→CCC)  prpD → 2‑methylcitrate dehydratase
JC JC 458,790 IS186 (–) +6 bp :: Δ1 bp 52.4% intergenic (+90/‑93) clpX → / → lon ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La
RA 602,200 A→G 17.7% E81G (GAG→GGG)  pheP → phenylalanine transporter
RA 644,420 A→C 17.6% V195G (GTG→GGG)  rna ← ribonuclease I
RA 715,338 T→A 15.5% intergenic (+140/‑74) pgm → / → ybfP phosphoglucomutase/lipoprotein
RA 1,196,131 G→A 20.3% A337T (GCC→ACC)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA 1,196,305 C→T 53.3% R395C (CGT→TGT)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
JC JC 1,293,032 IS1 (–) +8 bp 100% intergenic (‑110/‑488) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
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 1,325,980 A→T 16.0% Y412F (TAC→TTC)  yciQ → enhancer of membrane protein expression; putative inner membrane protein
RA 1,445,981 T→G 29.3% G34G (GGT→GGG)  ydbL → DUF1318 family protein
RA 1,695,755 T→C 14.8% E106G (GAG→GGG)  uidA ← beta‑D‑glucuronidase
JC JC 1,979,486 IS5 (+) +4 bp 100% intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 2,079,975 A→G 18.9% L206P (CTC→CCC)  yeeA ← putative transporter, FUSC family inner membrane protein
RA 2,132,787 A→C 100% I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
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 2,235,398 T→G 24.5% V45G (GTG→GGG)  preA → dihydropyrimidine dehydrogenase, NADH‑dependent, subunit C
RA 2,525,298 C→T 13.5% L58F (CTT→TTT)  yfeN → putative outer membrane protein
RA 2,909,229 A→C 32.3% G146G (GGT→GGG)  pyrG ← CTP synthetase
RA 3,079,070 A→C 13.3% G87G (GGT→GGG)  cmtB ← putative mannitol‑specific enzyme IIA component of PTS
RA 3,206,438 G→A 26.6% intergenic (‑182/‑25) ttdR ← / → ttdA transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
RA 3,527,722 A→C 15.5% S418S (TCA→TCC)  yrfF → putative RcsCDB‑response attenuator, inner membrane protein
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 3,665,698 T→C 24.0% D38G (GAT→GGT)  gadX ← acid resistance regulon transcriptional activator; autoactivator
RA 3,741,500 T→C 13.1% E28G (GAG→GGG)  ysaA ← putative hydrogenase, 4Fe‑4S ferredoxin‑type component
RA 3,749,429 T→G 19.8% G66G (GGT→GGG)  sgbU → putative L‑xylulose 5‑phosphate 3‑epimerase
RA 3,767,039 A→T 6.1% N235Y (AAT→TAT)  yibA → putative immunity protein for polymorphic toxin RhsA; HEAT‑domain protein; lethality reduction protein
RA 3,790,969 A→C 10.0% V126G (GTG→GGG)  tdh ← L‑threonine 3‑dehydrogenase, NAD(P)‑binding
MC JC 3,815,859 Δ82 bp 100% [rph]–[rph] [rph], [rph]
RA 3,857,245 T→C 8.3% D387G (GAT→GGT)  yidJ ← sulfatase/phosphatase superfamily protein
JC 4,001,645 Δ5 bp 100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,015,351 T→C 13.9% intergenic (+37/+3) metE → / ← ysgA 5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase/putative carboxymethylenebutenolidase
RA 4,065,580 T→A 13.4% T63S (ACC→TCC)  yihO ← putative sulphoquinovose importer
RA 4,125,340 T→G 19.1% T491P (ACC→CCC)  priA ← Primosome factor n' (replication factor Y)
RA 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,241,829 T→A 12.7% L142F (TTA→TTT)  xylE ← D‑xylose transporter
RA 4,253,509 T→G 12.0% V165G (GTG→GGG)  ubiA → p‑hydroxybenzoate octaprenyltransferase
RA 4,253,517 A→G 11.9% S168G (AGT→GGT)  ubiA → p‑hydroxybenzoate octaprenyltransferase
RA 4,296,060 C→T 20.9% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,379:2 +C 6.1% intergenic (+585/+57) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,380:1 +C 90.8% intergenic (+586/+56) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,380:2 +G 90.8% intergenic (+586/+56) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,370,192 T→G 23.1% H74P (CAC→CCC)  yjeH ← putative transporter
RA 4,386,017 G→T 13.1% *105L (TGA→TTA)  yjeO → inner membrane protein
RA 4,430,339 A→G 20.8% E159G (GAG→GGG)  cycA → D‑alanine/D‑serine/glycine transporter
RA 4,464,859 A→C 15.6% V441G (GTG→GGG)  treB ← trehalose‑specific PTS enzyme: IIB and IIC component
RA 4,480,111 C→T 13.3% L128F (CTC→TTC)  yjgN → DUF898 family inner membrane protein
RA 4,596,480 A→G 23.9% E164G (GAG→GGG)  lgoD → L‑galactonate oxidoreductase; L‑gulonate oxidoreductase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 299986 300198 213 12 [11] [11] 13 paoC PaoABC aldehyde oxidoreductase, Moco‑containing subunit
* * ÷ NC_000913 752875 753083 209 12 [11] [11] 12 ybgD/gltA putative fimbrial‑like adhesin protein/citrate synthase
* * ÷ NC_000913 2192252 2192435 184 12 [11] [11] 13 yehD/yehE putative fimbrial‑like adhesin protein/DUF2574 family protein
* * ÷ NC_000913 2469145 2469771 627 12 [11] [10] 13 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ NC_000913 2470094 2470359 266 13 [9] [11] 12 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ NC_000913 3423855–3424434 3424434 1–580 12 [10] [7] 13 [rrlD] [rrlD]
* * ÷ NC_000913 3769578 3769899 322 18 [9] [7] 12 [yibV]–yibV [yibV],yibV
* * ÷ NC_000913 3793657 3793746 90 12 [10] [10] 14 [yibB] [yibB]
* * ÷ NC_000913 4233773 4235438 1666 12 [10] [11] 12 [pgi] [pgi]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1049781 =NA (NA)3 (0.050)
+CCC		 3/412 NT 75.3% noncoding (4/768 nt) IS1 repeat region
?NC_000913 1293032 = 1 (0.020)intergenic (‑110/‑495) hns/tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
* ? NC_000913 1207790 =5 (0.090)60 (1.140) 40/386 NT 89.8% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 9 (0.170)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12078055 (0.090)53 (1.010) 36/386 NT 88.6% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 9 (0.170)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 19785020 (0.000)39 (0.710) 32/402 NT 100% intergenic (‑305/+16) flhD/insB1 flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
?NC_000913 1979279 = 0 (0.000)intergenic (‑64/‑474) insA/uspC IS1 repressor TnpA/universal stress protein