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 186,409 C→T 34.3% A748T (GCG→ACG)  glnD ← uridylyltransferase
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 409,139 A→T 5.1% I294N (ATT→AAT)  rdgC ← nucleoid‑associated ssDNA and dsDNA binding protein; competitive inhibitor of RecA function
RA 581,640 A→T 5.0% pseudogene (287/309 nt) aaaD → pseudogene; DLP12 prophage; tail fiber assembly protein family;Phage or Prophage Related
JC 759,508 (TGAACGTGCTGG)2→1 10.1% coding (803‑814/2802 nt) sucA → 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding
RA 759,906 G→A 15.2% D401N (GAT→AAT)  sucA → 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding
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
RA 1,466,856 A→G 5.5% pseudogene (1465/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,735,587 G→A 5.1% Q70Q (CAG→CAA sodB → superoxide dismutase, Fe
RA 1,887,917 T→A 7.1% I25I (ATA→ATT rnd ← ribonuclease D
JC JC 1,979,486 IS5 (+) +4 bp 100% intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 2,048,541 A→T 6.2% T1202S (ACC→TCC)  yeeJ → putative adhesin
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
JC JC 2,269,907 IS5 (–) +4 bp 7.9% intergenic (+340/‑69) lpxT → / → mepS lipid A 1‑diphosphate synthase; undecaprenyl pyrophosphate:lipid A 1‑phosphate phosphotransferase/murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein, weak murein LD‑carboxypeptidase
RA 2,304,798 T→C 11.8% intergenic (+405/+310) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,370,205 G→A 5.2% R63H (CGC→CAC)  arnD → undecaprenyl phosphate‑alpha‑L‑ara4FN deformylase
RA 2,426,951 A→G 5.2% intergenic (‑163/+58) hisJ ← / ← argT histidine ABC transporter periplasmic binding protein/lysine/arginine/ornithine transporter subunit
RA 2,876,426 G→A 78.1% intergenic (‑97/‑155) cysD ← / → iap sulfate adenylyltransferase, subunit 2/aminopeptidase in alkaline phosphatase isozyme conversion
RA 3,437,649 G→A 9.3% A378T (GCA→ACA)  trkA → NAD‑binding component of TrK potassium transporter
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
MC JC 3,815,859 Δ82 bp 100% [rph][rph] [rph], [rph]
MC JC 4,001,645 Δ5 bp 100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,296,060 C→T 19.2% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,268 T→C 26.7% intergenic (+474/+168) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,286 C→T 20.9% intergenic (+492/+150) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,303 A→G 13.0% intergenic (+509/+133) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,304 A→C 11.5% intergenic (+510/+132) 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

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 754988 758442 3455 34 [33] [33] 35 sdhC–sdhB sdhC,sdhD,sdhA,sdhB
* * ÷ NC_000913 1529977 1530472 496 34 [33] [30] 34 [ydcD] [ydcD]
* * ÷ NC_000913 3423801–3424231 3424404–3424239 9–604 34 [33] [26] 35 [rrlD] [rrlD]
* * ÷ NC_000913 3769461 3770009 549 35 [33] [33] 35 [yibV]–[yibU] [yibV],yibV,[yibU]
* * ÷ NC_000913 3798553 3800349 1797 34 [32] [31] 35 [waaU]–[waaY] [waaU],waaZ,[waaY]
* * ÷ NC_000913 3804143 3805220 1078 36 [33] [32] 34 waaS–[waaP] waaS,[waaP]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 75476321 (0.250)8 (0.100) 8/512 NT 28.8% intergenic (‑295/‑414) gltA/sdhC citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556
?NC_000913 755100 = 19 (0.230)intergenic (‑632/‑77) gltA/sdhC citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556
* ? NC_000913 1207790 =37 (0.440)46 (0.580) 34/490 NT 53.9% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 44 (0.550)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780537 (0.440)34 (0.430) 28/490 NT 46.3% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 44 (0.550)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 124257888 (1.040)5 (0.060)
+T
5/520 NT 5.4% coding (503/915 nt) ldcA murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A
?NC_000913 = 1242591 87 (1.020)coding (490/915 nt) ldcA murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A
* ? NC_000913 = 12994980 (0.000)10 (0.120) 8/514 NT 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 1303239 =39 (0.460)54 (0.640) 43/522 NT 58.1% coding (341/921 nt) oppB oligopeptide ABC transporter permease
?NC_000913 = 1979270 NA (NA)noncoding (1/768 nt) IS1 repeat region
* ? NC_000913 = 19785020 (0.000)36 (0.440) 31/506 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