breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 177,549 G→A 7.0% R26C (CGT→TGT)  yadS ← UPF0126 family inner membrane protein
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 262,732:1 +G 5.4% coding (1230/1254 nt) proA → gamma‑glutamylphosphate reductase
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 762,841 G→T 6.4% intergenic (+102/‑173) sucB → / → sucC dihydrolipoyltranssuccinase/succinyl‑CoA synthetase, beta subunit
RA 876,148 C→T 13.8% R272C (CGC→TGC)  yliF → putative membrane‑anchored diguanylate cyclase
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 1,466,438 T→G 10.7% pseudogene (1047/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,498,623 Δ1 bp 6.6% intergenic (+112/‑28) opgD → / → ydcH OPG biosynthetic periplasmic protein/DUF465 family protein
RA 1,501,720 T→A 8.4% Y53* (TAT→TAA tehB → tellurite, selenium methyltransferase, SAM‑dependent; tellurite, selenium resistance protein
RA 1,612,932 T→A 6.1% E107V (GAG→GTG)  glsB ← glutaminase 2
JC 1,619,080 Δ35 bp 25.9% intergenic (‑172/‑6) marC ← / → marR UPF0056 family inner membrane protein/transcriptional repressor of multiple antibiotic resistance
RA 1,936,648 C→T 62.2% intergenic (‑334/‑4) zwf ← / → yebK glucose‑6‑phosphate 1‑dehydrogenase/putative DNA‑binding transcriptional regulator
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 2,132,787 A→C 100% I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
RA 2,151,859 A→G 9.5% F205S (TTT→TCT)  yegK ← ser/thr phosphatase‑related protein
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
JC 2,413,513 Δ10 bp 20.1% coding (44‑53/1203 nt) ackA → acetate kinase A and propionate kinase 2
JC 2,526,111 Δ3 bp 5.1% coding (744‑746/927 nt) yfeR ← transcriptional regulator of yefH
RA 3,213,426 T→G 40.3% I127S (ATC→AGC)  rpoD → RNA polymerase, sigma 70 (sigma D) factor
RA 3,361,441 C→T 13.8% A89V (GCA→GTA)  gltF → periplasmic 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 3,729,754 A→G 6.4% F338L (TTC→CTC)  xylA ← D‑xylose isomerase
MC JC 3,815,859 Δ82 bp 100% [rph][rph] [rph], [rph]
JC 4,001,645 Δ5 bp 100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,011,944 A→T 5.8% D290V (GAT→GTT) 
D291E (GAT→GAA
yigM →
metR ←
putative inner membrane EamA‑like transporter
methionine biosynthesis regulon transcriptional regulator
JC JC 4,049,859 IS2 (–) +5 bp 82.7% intergenic (+107/‑36) polA → / → spf 5' to 3' DNA polymerase and 3' to 5'/5' to 3' exonuclease/Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent
JC 4,049,991 Δ12 bp 40.7% noncoding (93‑104/109 nt) spf → Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent
RA 4,157,050 A→G 5.4% E67E (GAA→GAG argH → argininosuccinate lyase
RA 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,296,190 A→G 17.7% intergenic (+396/+246) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,191 A→C 18.2% intergenic (+397/+245) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,268 T→C 25.0% intergenic (+474/+168) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,286 C→T 12.9% intergenic (+492/+150) 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 4,308,355 G→T 22.1% L42M (CTG→ATG)  alsE ← allulose‑6‑phosphate 3‑epimerase
RA 4,326,048 G→A 8.3% intergenic (‑307/+351) yjdN ← / ← yjdM metalloprotein superfamily protein/zinc‑ribbon family protein
RA 4,326,088 T→G 15.4% intergenic (‑347/+311) yjdN ← / ← yjdM metalloprotein superfamily protein/zinc‑ribbon family protein
RA 4,629,274 T→G 5.8% I417L (ATC→CTC)  ettA ← energy‑dependent translational throttle A

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 2990844 2991370 527 20 [15] [15] 16 [ygeF]–[ygeG] [ygeF],ygeF,[ygeG]
* * ÷ NC_000913 3423894–3424233 3424402–3424239 7–509 17 [15] [15] 17 rrlD 23S ribosomal RNA of rrnD operon
* * ÷ NC_000913 4233700 4235471 1772 16 [15] [15] 17 pgi pgi

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =17 (0.290)29 (0.520) 28/474 NT 64.5% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 16 (0.290)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780516 (0.270)45 (0.810) 39/474 NT 74.4% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 16 (0.290)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 1397238NA (NA)9 (0.150) 9/506 NT 18.0% noncoding (1195/1195 nt) IS5 repeat region
?NC_000913 = 2101469 41 (0.690)pseudogene (276/349 nt) wbbL pseudogene, lipopolysaccharide biosynthesis protein
* ? NC_000913 = 184062172 (1.210)4 (0.070) 4/500 NT 6.2% coding (1155/1308 nt) ynjE molybdopterin synthase sulfurtransferase
?NC_000913 = 1841095 50 (0.850)coding (309/621 nt) ynjF CDP‑alcohol phosphatidyltransferase family inner membrane protein
* ? NC_000913 1928538 =52 (0.870)4 (0.070) 3/492 NT 6.9% coding (302/2061 nt) ptrB protease II
?NC_000913 1928806 = 58 (1.000)coding (34/2061 nt) ptrB protease II
* ? NC_000913 = 313541365 (1.090)4 (0.070) 3/488 NT 5.4% coding (959/1500 nt) pitB phosphate transporter
?NC_000913 = 3135486 77 (1.340)coding (886/1500 nt) pitB phosphate transporter