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 71,877 A→G 27.2% E176G (GAG→GGG)  yabI → DedA family inner membrane protein
RA 191,662 A→G 9.4% E269G (GAG→GGG)  tsf → translation elongation factor EF‑Ts
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 272,543 T→G 15.1% intergenic (+354/‑37) insN → / → eyeA pseudogene, IS911 transposase A;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/novel sRNA, function unknown, CP4‑6 propahge
RA 433,649 T→G 45.0% G65G (GGT→GGG)  ribD → fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil 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 921,692 T→G 19.9% V449G (GTG→GGG)  macB → macrolide ABC transporter peremase/ATPase
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 1,466,856 A→G 12.4% pseudogene (1465/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
JC 1,619,080 Δ35 bp 12.3% intergenic (‑172/‑6) marC ← / → marR UPF0056 family inner membrane protein/transcriptional repressor of multiple antibiotic resistance
JC JC 1,979,486 IS5 (+) +4 bp 100% intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 2,024,816 A→C 16.6% V3G (GTG→GGG)  dsrB ← uncharacterized protein
RA 2,045,276 T→C 7.9% D113D (GAT→GAC)  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
RA 2,849,865 T→G 19.9% intergenic (‑16/+109) hycB ← / ← hycA hydrogenase 3, Fe‑S subunit/regulator of the transcriptional regulator FhlA
RA 2,874,505 T→C 15.6% G305G (GGA→GGG)  cysN ← sulfate adenylyltransferase, subunit 1
RA 2,875,269 T→G 18.5% T51P (ACC→CCC)  cysN ← sulfate adenylyltransferase, subunit 1
RA 3,053,515 T→C 26.8% S2G (AGC→GGC) 
*442W (TGA→TGG) 		 ubiH ←
pepP ←		 2‑octaprenyl‑6‑methoxyphenol hydroxylase, FAD/NAD(P)‑binding
proline aminopeptidase P II
RA 3,053,526 T→C 28.3% R439G (AGA→GGA)  pepP ← proline aminopeptidase P II
RA 3,064,900 G→C 12.4% S33S (TCG→TCC)  scpC → propionyl‑CoA:succinate CoA transferase
RA 3,210,861 T→G 17.1% G27G (GGT→GGG)  rpsU → 30S ribosomal subunit protein S21
RA 3,346,885 C→T 6.1% P103L (CCG→CTG)  ptsN → sugar‑specific enzyme IIA component of PTS
RA 3,355,507 G→C 20.3% P261P (CCG→CCC)  gltB → glutamate synthase, large subunit
JC 3,525,959 +GGATCA 83.2% coding (191/561 nt) nudE ← adenosine nucleotide hydrolase; Ap3A/Ap2A/ADP‑ribose/NADH hydrolase
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 3,629,382 T→C 23.4% S53G (AGC→GGC)  rbbA ← ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein
MC JC 3,815,859 Δ82 bp 100% [rph]–[rph] [rph], [rph]
RA 3,838,902 C→T 11.1% L219L (CTG→TTG)  yicL → EamA family inner membrane putative transporter
RA 3,842,368 A→C 28.3% V12G (GTG→GGG)  yicN ← DUF1198 family protein
RA 3,951,495 T→G 17.1% pseudogene (936/984 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 4,065,604 T→A 27.8% I55F (ATC→TTC)  yihO ← putative sulphoquinovose importer
RA 4,125,363 T→G 26.1% H483P (CAC→CCC)  priA ← Primosome factor n' (replication factor Y)
RA 4,158,653 T→G 18.6% V55G (GTG→GGG)  oxyR → oxidative and nitrosative stress transcriptional regulator
RA 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,244,539 A→G 20.2% N179N (AAT→AAC)  malF ← maltose transporter subunit
RA 4,295,700 T→G 20.8% V407G (GTG→GGG)  gltP → glutamate/aspartate:proton symporter
RA 4,296,060 C→T 32.7% 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 4,609,767 T→G 24.6% G118G (GGT→GGG)  prfC → peptide chain release factor RF‑3

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 156971 157261 291 11 [10] [10] 11 [folK] [folK]
* * ÷ NC_000913 299949 300209 261 11 [10] [10] 11 paoC PaoABC aldehyde oxidoreductase, Moco‑containing subunit
* * ÷ NC_000913 384825 385057 233 11 [10] [10] 11 yaiS/tauA putative PIG‑L family deacetylase/taurine ABC transporter periplasmic binding protein
* * ÷ NC_000913 583137 584247 1111 11 [10] [10] 11 [appY] [appY]
* * ÷ NC_000913 720912 721157 246 11 [10] [10] 11 [kdpE] [kdpE]
* * ÷ NC_000913 997547 997804 258 12 [10] [9] 11 ssuE/elfA NAD(P)H‑dependent FMN reductase/laminin‑binding fimbrin subunit
* * ÷ NC_000913 1212019 1212618 600 11 [10] [10] 11 iraM/ycgX RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein
* * ÷ NC_000913 1216387 1216703 317 11 [10] [8] 11 [ariR] [ariR]
* * ÷ NC_000913 1230387 1230566 180 12 [10] [10] 11 [hlyE] [hlyE]
* * ÷ NC_000913 1423639 1423845 207 11 [10] [10] 11 [rzpR]–[trkG] [rzpR],[trkG]
* * ÷ NC_000913 1530042 1530400 359 11 [10] [10] 11 ydcD putative immunity protein for RhsE
* * ÷ NC_000913 1586550 1586754 205 11 [10] [10] 11 ydeP/ydeQ putative oxidoreductase/putative fimbrial‑like adhesin protein
* * ÷ NC_000913 1598184 1598376 193 11 [10] [10] 11 yneO/lsrK pseudogene, AidA homolog/autoinducer‑2 (AI‑2) kinase
* * ÷ NC_000913 1640625 1641039 415 11 [10] [10] 11 essQ/cspB Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
* * ÷ NC_000913 1754673 1754986 314 11 [9] [10] 11 [ydhZ] [ydhZ]
* * ÷ NC_000913 1812740 1813311 572 12 [10] [8] 11 [ydjO] [ydjO]
* * ÷ NC_000913 1907935 1908147 213 12 [10] [10] 13 yobF/yebO DUF2527 family heat‑induced protein/putative inner membrane protein
* * ÷ NC_000913 2056626 2056831 206 11 [10] [10] 12 amn/yeeN AMP nucleosidase/UPF0082 family protein
* * ÷ NC_000913 2469244 2469778 535 11 [10] [10] 11 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ NC_000913 2470094 2470473 380 11 [6] [9] 11 [gtrS] [gtrS]
* * ÷ NC_000913 2774845 2774989 145 11 [10] [9] 12 yfjW CP4‑57 prophage; putative inner membrane protein
* * ÷ NC_000913 2786020 2786625 606 11 [10] [10] 14 [ygaQ] [ygaQ]
* * ÷ NC_000913 2995105 2995332 228 12 [9] [10] 11 [ygeN] [ygeN]
* * ÷ NC_000913 3268274 3268446 173 11 [10] [10] 11 [yhaB]–[yhaC] [yhaB],[yhaC]
* * ÷ NC_000913 3284083 3284187 105 11 [9] [9] 15 [agaB] [agaB]
* * ÷ NC_000913 3287075 3287422 348 11 [10] [7] 11 agaI/yraH galactosamine‑6‑phosphate isomerase/putative fimbrial‑like adhesin protein
* * ÷ NC_000913 3423865–3424455 3424455 1–591 11 [10] [9] 11 [rrlD] [rrlD]
* * ÷ NC_000913 3455424 3455682 259 13 [10] [10] 11 [gspC] [gspC]
* * ÷ NC_000913 3653652 3653794 143 11 [10] [10] 13 [yhiS] [yhiS]
* * ÷ NC_000913 3769623 3770073 451 11 [10] [10] 11 [yibV]–[yibU] [yibV],yibV,yibU,[yibU]
* * ÷ NC_000913 3804231 3804552 322 12 [10] [10] 11 waaS lipopolysaccharide rhamnose:KdoIII transferase; lipopolysaccharide core biosynthesis protein
* * ÷ NC_000913 3804712 3805191 480 11 [10] [9] 12 [waaS]–[waaP] [waaS],[waaP]
* * ÷ NC_000913 4233750 4235455 1706 12 [9] [10] 11 pgi pgi
* * ÷ NC_000913 4282667 4282869 203 12 [8] [10] 11 yjcF pentapeptide repeats protein
* * ÷ NC_000913 4476743 4477164 422 11 [9] [8] 14 yjgL SopA‑central‑domain‑like hexapeptide repeat protein
* * ÷ NC_000913 4541558 4541921 364 12 [10] [10] 11 [fimB] [fimB]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 120777913 (0.260)4 (0.080)
+TTCGAAAACC		 4/394 NT 37.5% coding (279/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209618 1 (0.020)pseudogene (2/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 1207790 =13 (0.260)38 (0.820) 31/382 NT 85.4% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 1 (0.020)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780513 (0.260)41 (0.890) 32/382 NT 86.3% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 1 (0.020)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 19785020 (0.000)20 (0.420) 18/398 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