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 28,116 T→A 6.2% L275Q (CTG→CAG)  rihC → ribonucleoside hydrolase 3
JC 186,134 +CCC 10.2% coding (2517/2673 nt) glnD ← uridylyltransferase
RA 235,917 C→T 5.3% R29H (CGC→CAC)  rnhA ← ribonuclease HI, degrades RNA of DNA‑RNA hybrids
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 485,039 A→G 5.1% L194S (TTG→TCG)  acrA ← multidrug efflux system
RA 524,811 G→A 5.3% A517A (GCG→GCA rhsD → Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA 753,730 C→T 8.7% A247T (GCG→ACG)  gltA ← citrate synthase
RA 759,776 C→A 59.0% D357E (GAC→GAA sucA → 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding
RA 761,422 C→T 9.3% A906V (GCC→GTC)  sucA → 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding
RA 864,741 Δ1 bp 5.3% coding (389/750 nt) moeB ← molybdopterin synthase sulfurylase
RA 927,611 Δ1 bp 6.5% coding (1585/1722 nt) cydC ← glutathione/cysteine ABC transporter export permease/ATPase
RA 966,796 C→T 5.9% T59I (ACA→ATA)  msbA → lipid ABC transporter permease/ATPase
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 1,963,203 G→A 8.2% G616G (GGC→GGT flhA ← putative flagellar export pore protein
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 2,173,361 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 2,389,401 IS2 (+) +5 bp 50.0% coding (286‑290/849 nt) yfbP → TPR‑like repeats‑containing protein
RA 2,846,101 A→G 5.1% L124S (TTG→TCG)  hycE ← hydrogenase 3, large subunit
RA 2,876,376 G→T 20.0% intergenic (‑47/‑205) cysD ← / → iap sulfate adenylyltransferase, subunit 2/aminopeptidase in alkaline phosphatase isozyme conversion
JC JC 2,876,678 IS5 (+) +4 bp 63.2% coding (98‑101/1038 nt) iap → aminopeptidase in alkaline phosphatase isozyme conversion
RA 2,974,291 Δ1 bp 8.0% coding (1724/2160 nt) aas ← fused 2‑acylglycerophospho‑ethanolamine acyl transferase/acyl‑acyl carrier protein synthetase
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 3,665,444 A→G 12.5% S123P (TCT→CCT)  gadX ← acid resistance regulon transcriptional activator; autoactivator
MC JC 3,815,859 Δ82 bp 100% [rph][rph] [rph], [rph]
RA 3,951,561 C→T 40.1% pseudogene (20/663 nt) ilvG → pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted
MC JC 4,001,645 Δ5 bp 100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,031,045 T→C 9.1% intergenic (‑74/‑116) fadB ← / → pepQ fused 3‑hydroxybutyryl‑CoA epimerase/delta(3)‑cis‑delta(2)‑trans‑enoyl‑CoA isomerase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase/proline dipeptidase
RA 4,125,618 Δ1 bp 5.5% coding (1193/2199 nt) priA ← Primosome factor n' (replication factor Y)
RA 4,125,619 Δ1 bp 5.5% coding (1192/2199 nt) priA ← Primosome factor n' (replication factor Y)
RA 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,296,060 C→T 10.9% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,190 A→G 28.3% intergenic (+396/+246) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,191 A→C 33.7% intergenic (+397/+245) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,268 T→C 21.0% intergenic (+474/+168) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,286 C→T 11.7% intergenic (+492/+150) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,303 A→G 7.5% intergenic (+509/+133) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,304 A→C 6.3% 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 384794 385094 301 12 [11] [11] 12 yaiS/tauA putative PIG‑L family deacetylase/taurine ABC transporter periplasmic binding protein
* * ÷ NC_000913 755143 758392 3250 13 [11] [10] 12 sdhC–[sdhB] sdhC,sdhD,sdhA,[sdhB]
* * ÷ NC_000913 1978480 1979326 847 12 [9] [10] 12 insB1–insA insB1,insA
* * ÷ NC_000913 2106433 2107407 975 13 [10] [11] 12 [wbbH]–[glf] [wbbH],[glf]
* * ÷ NC_000913 3423912–3424232 3424382–3424239 8–471 12 [11] [9] 13 rrlD 23S ribosomal RNA of rrnD operon
* * ÷ NC_000913 3798873 3799653 781 13 [11] [10] 14 [waaU]–[waaZ] [waaU],[waaZ]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 12040669 (1.290)4 (0.080) 4/494 NT 5.8% coding (1146/1374 nt) aroP aromatic amino acid transporter
?NC_000913 = 120807 61 (1.160)coding (745/1374 nt) aroP aromatic amino acid transporter
* ? NC_000913 231961 =46 (0.860)10 (0.190) 4/498 NT 17.3% coding (36/624 nt) yafE putative S‑adenosyl‑L‑methionine‑dependent methyltransferase
?NC_000913 232463 = 50 (0.940)coding (538/624 nt) yafE putative S‑adenosyl‑L‑methionine‑dependent methyltransferase
* ? NC_000913 = 24300979 (1.470)5 (0.100) 3/488 NT 6.8% coding (295/2445 nt) fadE acyl coenzyme A dehydrogenase
?NC_000913 = 243192 60 (1.150)coding (112/2445 nt) fadE acyl coenzyme A dehydrogenase
* ? NC_000913 = 258675NA (NA)9 (0.170) 8/502 NT 20.9% noncoding (1/768 nt) IS1 repeat region
?NC_000913 1303476 = 34 (0.630)coding (578/921 nt) oppB oligopeptide ABC transporter permease
* ? NC_000913 381463 =NA (NA)3 (0.060) 3/480 NT NA noncoding (204/1331 nt) IS2 repeat region
?NC_000913 381851 = NA (NA)noncoding (592/1331 nt) IS2 repeat region
* ? NC_000913 762116 =61 (1.140)7 (0.140) 4/474 NT 9.5% coding (595/1218 nt) sucB dihydrolipoyltranssuccinase
?NC_000913 762340 = 75 (1.480)coding (819/1218 nt) sucB dihydrolipoyltranssuccinase
* ? NC_000913 934793 =81 (1.510)4 (0.080) 4/490 NT 5.4% coding (1570/3990 nt) ftsK DNA translocase at septal ring sorting daughter chromsomes
?NC_000913 935128 = 60 (1.150)coding (1905/3990 nt) ftsK DNA translocase at septal ring sorting daughter chromsomes
* ? NC_000913 1207790 =16 (0.300)20 (0.400) 19/470 NT 54.8% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 18 (0.360)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780516 (0.300)26 (0.520) 20/470 NT 61.2% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 18 (0.360)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 140732351 (0.950)4 (0.080) 4/482 NT 6.6% coding (473/1233 nt) ydaM diguanylate cyclase, csgD regulator
?NC_000913 = 1407695 64 (1.240)coding (101/1233 nt) ydaM diguanylate cyclase, csgD regulator
* ? NC_000913 1603870 =81 (1.510)4 (0.080) 4/482 NT 5.8% coding (852/1029 nt) lsrC autoinducer 2 import system permease protein
?NC_000913 1604608 = 51 (0.990)coding (562/993 nt) lsrD autoinducer 2 import system permease protein
* ? NC_000913 = 170988975 (1.400)4 (0.080) 4/496 NT 5.8% coding (748/1059 nt) rsxD SoxR iron‑sulfur cluster reduction factor component; putative membrane protein of electron transport complex
?NC_000913 = 1710391 56 (1.060)coding (188/621 nt) rsxG SoxR iron‑sulfur cluster reduction factor component; putative membrane protein of electron transport complex
* ? NC_000913 = 19785020 (0.000)9 (0.170) 8/486 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
* ? NC_000913 2077808 =52 (0.970)8 (0.160) 6/478 NT 14.9% coding (240/375 nt) cbtA CP4‑44 prophage; toxin of the YeeV‑YeeU toxin‑antitoxin system
?NC_000913 2077982 = 42 (0.820)pseudogene (43/168 nt) yeeW CP4‑44 prophage; uncharacterized protein;Phage or Prophage Related
* ? NC_000913 = 219000746 (0.860)3 (0.060) 3/496 NT 8.6% coding (904/2481 nt) yehB putative outer membrane protein
?NC_000913 = 2190342 18 (0.340)coding (569/2481 nt) yehB putative outer membrane protein
* ? NC_000913 = 222050656 (1.040)3 (0.060) 3/486 NT 5.4% coding (1484/2298 nt) bglX beta‑D‑glucoside glucohydrolase, periplasmic
?NC_000913 = 2220838 51 (0.980)coding (1152/2298 nt) bglX beta‑D‑glucoside glucohydrolase, periplasmic
* ? NC_000913 = 249168821 (0.390)3 (0.060) 3/490 NT 7.4% coding (263/1695 nt) oxc oxalyl CoA decarboxylase, ThDP‑dependent
?NC_000913 = 2492132 55 (1.050)coding (1123/1251 nt) frc formyl‑CoA transferase, NAD(P)‑binding
* ? NC_000913 = 270746345 (0.840)4 (0.080) 4/490 NT 8.2% coding (339/480 nt) rseC SoxR iron‑sulfur cluster reduction factor component
?NC_000913 = 2707650 46 (0.880)coding (152/480 nt) rseC SoxR iron‑sulfur cluster reduction factor component
* ? NC_000913 3620759 =NA (NA)5 (0.100) 5/486 NT 9.7% coding (1568/4236 nt) rhsB Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
?NC_000913 3621156 = 48 (0.890)coding (1965/4236 nt) rhsB Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
* ? NC_000913 3955668 =72 (1.340)5 (0.100) 4/486 NT 8.2% coding (338/1545 nt) ilvA l‑threonine dehydratase, biosynthetic; also known as threonine deaminase
?NC_000913 3955897 = 42 (0.810)coding (567/1545 nt) ilvA l‑threonine dehydratase, biosynthetic; also known as threonine deaminase
* ? NC_000913 4056977 =70 (1.300)4 (0.080) 4/492 NT 5.6% coding (1058/1410 nt) glnA glutamine synthetase
?NC_000913 4057252 = 67 (1.270)coding (783/1410 nt) glnA glutamine synthetase
* ? NC_000913 = 450085849 (0.910)4 (0.080) 4/492 NT 8.6% intergenic (‑67/‑402) yjgX/yjgZ pseudogene fragment/uncharacterized protein
?NC_000913 = 4500949 37 (0.700)intergenic (‑158/‑311) yjgX/yjgZ pseudogene fragment/uncharacterized protein
* ? NC_000913 4513936 =46 (0.860)3 (0.060) 3/480 NT 5.3% coding (373/903 nt) fecB ferric citrate ABC transporter periplasmic binding protein
?NC_000913 4514562 = 63 (1.230)coding (2116/2325 nt) fecA TonB‑dependent outer membrane ferric citrate transporter and signal transducer; ferric citrate extracelluar receptor; FecR‑interacting protein