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
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 278,652 G→T 6.7% L51M (CTG→ATG)  afuC ← CP4‑6 prophage; putative ferric transporter subunit
RA 320,423 T→G 12.9% V66G (GTG→GGG)  rclR → reactive chlorine species (RCS)‑specific activator of the rcl genes
JC JC 458,790 IS186 (–) +6 bp :: Δ1 bp 100% intergenic (+90/‑93) clpX → / → lon ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La
RA 525,571 T→G 14.9% W771G (TGG→GGG)  rhsD → Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA 540,546 C→T 12.5% intergenic (+38/‑19) allB → / → ybbY allantoinase/putative uracil/xanthine transporter
RA 1,061,965 A→G 35.1% E56G (GAG→GGG)  torD → TorA‑maturation chaperone
RA 1,196,305 C→T 100% 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 1,445,981 T→G 31.7% G34G (GGT→GGG ydbL → DUF1318 family protein
JC 1,707,847 Δ10 bp 19.1% coding (929‑938/2223 nt) rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,709,179:1 +C 14.3% coding (38/1059 nt) rsxD → SoxR iron‑sulfur cluster reduction factor component; putative membrane protein of electron transport complex
RA 1,878,707 A→C 10.9% T331T (ACA→ACC yeaP → diguanylate cyclase
MC JC 1,978,503 Δ776 bp 100% insB1insA insB1, insA
JC JC 1,979,486 IS5 (+) +4 bp 100% intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 2,104,337 T→C 7.7% E58G (GAG→GGG)  wbbK ← lipopolysaccharide biosynthesis 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 2,283,059 C→A 13.6% D297Y (GAT→TAT)  yejK ← spermidine nucleoid‑associated protein
JC 2,391,259 +CAA 12.1% coding (247/1458 nt) nuoN ← NADH:ubiquinone oxidoreductase, membrane subunit N
RA 3,277,448 G→A 17.2% E38K (GAA→AAA)  yhaV → toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system
RA 3,289,078 C→A 21.9% Q89K (CAG→AAG)  yraJ → putative outer membrane protein
RA 3,327,171 A→C 15.1% V165G (GTG→GGG)  rlmE ← 23S rRNA U2552 2'‑O‑ribose methyltransferase, SAM‑dependent
RA 3,335,254 T→C 12.7% E414G (GAG→GGG)  murA ← UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase
JC 3,399,171 Δ3 bp 7.1% coding (806‑808/1104 nt) mreC ← cell wall structural complex MreBCD transmembrane component MreC
RA 3,507,168 T→C 15.7% S57G (AGC→GGC)  yhfT ← inner membrane protein
JC JC 3,560,227 IS5 (–) +4 bp 8.9% pseudogene (224‑227/606 nt) glpR ← pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
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 3,638,228 A→G 23.5% E196G (GAG→GGG)  pitA → phosphate transporter, low‑affinity; tellurite importer
RA 3,697,740 T→G 15.7% V428G (GTG→GGG)  bcsE → cellulose production protein
RA 3,699,266 T→A 7.1% N351K (AAT→AAA bcsG → DUF3260 family cellulose production inner membrane protein
RA 3,791,999 A→G 7.2% S185P (TCA→CCA)  kbl ← glycine C‑acetyltransferase
RA 3,792,340 G→A 10.2% S71F (TCT→TTT)  kbl ← glycine C‑acetyltransferase
RA 3,796,793 A→G 13.2% D272G (GAT→GGT)  waaC → ADP‑heptose:LPS heptosyl transferase I
MC JC 3,815,859 Δ82 bp 100% [rph][rph] [rph], [rph]
RA 3,817,496 T→G 10.7% V274G (GTG→GGG)  yicC → UPF0701 family protein
RA 3,832,077 G→A 5.8% V541M (GTG→ATG)  yicH → putative inner membrane‑anchored periplasmic AsmA family protein
JC 4,001,645 Δ5 bp 100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,056,115 A→C 20.7% G75G (GGT→GGG glnL ← sensory histidine kinase in two‑component regulatory system with GlnG
RA 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,242,022 C→A 12.2% C78F (TGC→TTC)  xylE ← D‑xylose transporter
RA 4,268,202 T→G 6.5% R363R (CGT→CGG tyrB → tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent
RA 4,277,820 G→T 6.4% G118* (GGA→TGA)  soxR → redox‑sensitive transcriptional activator of soxS; autorepressor
RA 4,296,060 C→T 20.2% 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 4,319,404 A→C 22.9% V68G (GTG→GGG)  phnJ ← carbon‑phosphorus lyase, SAM‑dependent
RA 4,368,930 C→T 11.5% G89G (GGC→GGT fxsA → suppressor of F exclusion of phage T7
RA 4,378,890 C→A 23.8% A19S (GCT→TCT)  ampC ← penicillin‑binding protein; beta‑lactamase, intrinsically weak
RA 4,530,174 T→A 12.0% I24F (ATC→TTC)  sgcC ← putative PTS system EIIC permease component
RA 4,588,079 A→C 20.1% W263G (TGG→GGG)  yjiA ← metal‑binding GTPase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 384825 385029 205 17 [11] [10] 15 yaiS/tauA putative PIG‑L family deacetylase/taurine ABC transporter periplasmic binding protein
* * ÷ NC_000913 1465098 1465315 218 14 [13] [13] 14 ynbG ynbG
* * ÷ NC_000913 2469267 2469547 281 15 [13] [10] 14 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ NC_000913 3799035 3799352 318 17 [9] [12] 14 [waaU]–[waaZ] [waaU],[waaZ]
* * ÷ NC_000913 4233776 4235396 1621 14 [13] [12] 20 pgi glucosephosphate isomerase

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =21 (0.290)81 (1.210) 58/378 NT 85.1% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 9 (0.130)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780520 (0.270)53 (0.790) 41/378 NT 79.4% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 9 (0.130)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 171041737 (0.510)3 (0.040) 3/408 NT 7.5% coding (214/621 nt) rsxG SoxR iron‑sulfur cluster reduction factor component; putative membrane protein of electron transport complex
?NC_000913 2101749 = NA (NA)noncoding (1195/1195 nt) IS5 repeat region