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 222,965 (A)8→7 coding (133/576 nt) gmhB → D,D‑heptose 1,7‑bisphosphate phosphatase
MC JC 257,908 Δ776 bp [crl] [crl]
RA 1,630,528 T→G Y129S (TAT→TCT)  ydfI ← putative NAD‑dependent D‑mannonate oxidoreductase
MC JC 1,978,503 Δ776 bp insB1–insA insB1, insA
RA 2,019,460 G→A V359I (GTC→ATC)  fliK → flagellar hook‑length control protein
RA 2,020,473 C→A N129K (AAC→AAA)  fliM → flagellar motor switching and energizing component
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
JC JC 2,375,828 IS186 (+) +4 bp coding (132‑135/963 nt) menC ← O‑succinylbenzoyl‑CoA synthase
RA 2,904,212 G→A intergenic (+838/+535) ygcE → / ← queE putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
RA 3,440,923 C→A G36V (GGC→GTC)  rpoA ← RNA polymerase, alpha subunit
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
JC JC 3,890,075 IS5 (–) +4 bp coding (1346‑1349/1416 nt) tnaA → tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,406,129 T→C intergenic (+144/‑61) purA → / → nsrR adenylosuccinate synthetase/nitric oxide‑sensitive repressor for NO regulon
RA 4,633,743 C→T M1M (ATG→ATA) † yjjX ← non‑canonical purine NTP phosphatase, ITPase/XTPase
JC JC 4,640,551 IS1 (–) +9 bp intergenic (+9/‑383) yjjY → / → yjtD uncharacterized protein/putative methyltransferase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 773047 774169 1123 16 [1] [13] 17 cydB cytochrome d terminal oxidase, subunit II
* * ÷ NC_000913 1037731 1039266 1536 15 [13] [14] 21 [cbdA] [cbdA]
* * ÷ NC_000913 1166067 1167388 1322 15 [13] [13] 15 [ndh] [ndh]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 374930 =NA (NA)21 (0.350) 7/190 2.5 24.2% noncoding (1/436 nt) REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences
?NC_000913 377522 = 72 (1.090)intergenic (+211/+13) yaiL/frmB DUF2058 family protein/S‑formylglutathione hydrolase
* ? NC_000913 = 12994980 (0.000)47 (0.550) 30/268 0.6 100% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913 = 246638466 (0.750)47 (0.610) 20/244 1.1 48.1% intergenic (+1/‑161) argW/intS tRNA‑Arg/CPS‑53 (KpLE1) prophage; putative prophage CPS‑53 integrase
?NC_000913 2476600 = 43 (0.550)intergenic (+2/+94) pawZ/dsdC tRNA‑OTHER/dsd operon activator; autorepressor