mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 61,802 | T→G | 6.7% | D488A (GAT→GCT) | rapA ← | RNA polymerase remodeling/recycling factor ATPase, RNA polymerase‑associated, ATP‑dependent RNA translocase |
| JC | 62,763:1 | (CGTGGCG)1→2 | 10.1% | coding (502/2907 nt) | rapA ← | RNA polymerase remodeling/recycling factor ATPase, RNA polymerase‑associated, ATP‑dependent RNA translocase |
| JC | 114,145 | (CGG)2→1 | 2.7% | coding (702‑704/1044 nt) | guaC → | GMP reductase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 341,232 | T→A | 3.3% | A36A (GCT→GCA) | yahJ → | putative metallo‑dependent hydrolase domain deaminase |
| RA | 457,681 | A→G | 3.8% | K86E (AAA→GAA) | clpX → | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease |
| RA | 526,982 | A→T | 6.5% | N1241I (AAT→ATT) | rhsD → | Rhs protein with DUF4329 family putative toxin domain, putative neighboring cell growth inhibitor |
| RA | 807,758 | T→C | 3.1% | Y51C (TAC→TGC) | ybhB ← | kinase inhibitor homolog, UPF0098 family |
| RA | 1,024,167 | T→A | 3.9% | E61V (GAA→GTA) | yccF ← | DUF307 family inner membrane protein |
| RA | 1,196,305 | C→T | 100% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,205,141 | C→T | 4.2% | pseudogene (738/1134 nt) | aaaE → | pseudogene, phage terminase protein A family, e14 prophage,Phage or Prophage Related |
| RA | 1,262,522 | T→A | 4.4% | N119I (AAT→ATT) | ispE ← | 4‑diphosphocytidyl‑2‑C‑methylerythritol kinase |
| RA | 1,273,648 | Δ1 bp | 5.3% | intergenic (‑49/‑136) | ychN ← / → ychO | putative sulfur relay protein/putative invasin |
| MC JC | 1,411,925 | Δ23,060 bp | 100% | [ttcA]–[ttcC] | 33 genes [ttcA], intR, ydaQ, ydaC, ralR, recT, recE, racC, ydaE, kilR, sieB, ydaF, ydaG, racR, ydaS, ydaT, ydaU, ydaV, ydaW, rzpR, rzoR, trkG, ynaK, ydaY, tmpR, lomR, insH1, lomR, stfR, tfaR, pinR, ynaE, [ttcC] |
|
| RA | 1,511,669 | G→A | 5.9% | A6T (GCC→ACC) | ydcS → | putative ABC transporter periplasmic binding protein |
| JC | 1,675,674 | (AGCCGC)2→1 | 26.9% | coding (682‑687/1389 nt) | pntB ← | pyridine nucleotide transhydrogenase, beta subunit |
| RA | 1,708,844 | C→G | 9.7% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,709,987 | C→T | 3.8% | G282G (GGC→GGT) | rsxD → | SoxR iron‑sulfur cluster reduction factor component, putative membrane protein of electron transport complex |
| RA | 1,750,268 | C→T | 6.4% | P27P (CCG→CCA) | ydhU ← | putative cytochrome b subunit of YdhYVWXUT oxidoreductase complex |
| RA | 1,950,588 | Δ1 bp | 5.0% | intergenic (‑66/‑244) | aspS ← / → yecD | aspartyl‑tRNA synthetase/isochorismatase family protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,141,846 | C→T | 4.3% | A124T (GCG→ACG) | dcd ← | deoxycytidine triphosphate deaminase, dCTP deaminase |
| RA | 2,233,947 | C→T | 9.1% | intergenic (+110/‑84) | yeiS → / → preT | DUF2542 family protein/dihydropyrimidine dehydrogenase, NADH‑dependent, subunit N |
| RA | 2,249,475 | G→A | 4.0% | Q48* (CAA→TAA) | yeiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,339,605 | A→G | 4.3% | H14R (CAC→CGC) | ubiG → | bifunctional 3‑demethylubiquinone‑9 3‑methyltransferase/ 2‑octaprenyl‑6‑hydroxy phenol methylase |
| RA | 2,468,901 | Δ1 bp | 8.9% | coding (690/921 nt) | gtrB → | CPS‑53 (KpLE1) prophage, bactoprenol glucosyl transferase |
| RA | 2,616,373 | T→A | 4.2% | F94L (TTT→TTA) | bepA → | OM protein maintenance and assembly metalloprotease and chaperone, periplasmic |
| RA | 2,716,295 | Δ1 bp | 3.8% | coding (153/384 nt) | grcA ← | autonomous glycyl radical cofactor |
| RA | 2,956,177 | C→T | 3.0% | P902P (CCG→CCA) | ptrA ← | protease III |
| RA | 3,033,245 | G→A | 3.1% | V61V (GTG→GTA) | idi → | isopentenyl diphosphate isomerase |
| RA | 3,214,413 | A→C | 100% | I457L (ATT→CTT) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,560,305 | G→A | 3.3% | pseudogene (147/606 nt) | glpR ← | pseudogene, DNA‑binding transcriptional repressor,regulator, Energy metabolism, carbon: Anaerobic respiration, repressor of the glp operon |
| RA | 3,681,935 | Δ1 bp | 3.5% | coding (5/1497 nt) | yhjJ ← | putative periplasmic M16 family chaperone |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,948,449 | (T)7→6 | 100% | coding (1520/1521 nt) | yifB ← | magnesium chelatase family protein and putative transcriptional regulator |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,049,885 | T→C | 100% | intergenic (+134/‑13) | 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 |
| RA | 4,160,853 | C→T | 47.8% | intergenic (‑64/‑270) | sthA ← / → fabR | pyridine nucleotide transhydrogenase, soluble/transcriptional repressor of fabA and fabB |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,295,833 | T→C | 9.7% | intergenic (+40/+604) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,059 | C→T | 13.2% | intergenic (+266/+378) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 32.9% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 33.2% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,398,815 | G→A | 3.2% | R468H (CGT→CAT) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,634,209 | G→T | 4.1% | D138Y (GAC→TAC) | ytjC → | phosphatase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423868–3424230 | 3424399–3424237 | 8–532 | 25 [24] | [23] 25 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4233741 | 4235471 | 1731 | 26 [24] | [24] 25 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 49 (0.580) | 43/508 | NT | 100% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 458787 = | 5 (0.060) | 80 (0.960) | 61/502 | NT | 94.2% | intergenic (+87/‑101) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | 608011 = | NA (NA) | intergenic (+23/‑54) | hokE/insL1 | toxic polypeptide, small/IS186 transposase | |||||
| * | ? | NC_000913 | = 458799 | 2 (0.020) | 71 (0.860) | 50/500 | NT | 97.3% | intergenic (+99/‑89) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | = 609347 | NA (NA) | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex | |||||
| * | ? | NC_000913 | 758637 = | 75 (0.890) | 3 (0.040) | 3/492 | NT | 4.2% | intergenic (+232/‑69) | sdhB/sucA | succinate dehydrogenase, FeS subunit/2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| ? | NC_000913 | 758657 = | 63 (0.770) | intergenic (+252/‑49) | sdhB/sucA | succinate dehydrogenase, FeS subunit/2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding | |||||
| * | ? | NC_000913 | 762116 = | 101 (1.200) | 8 (0.100) | 4/480 | NT | 7.2% | coding (595/1218 nt) | sucB | dihydrolipoyltranssuccinase |
| ? | NC_000913 | 762340 = | 110 (1.380) | coding (819/1218 nt) | sucB | dihydrolipoyltranssuccinase | |||||
| * | ? | NC_000913 | 1207790 = | 33 (0.390) | 24 (0.300) | 23/476 | NT | 46.6% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 24 (0.300) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 32 (0.380) | 41 (0.520) | 33/476 | NT | 60.3% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 24 (0.300) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 2 (0.020) | 57 (0.680) | 44/508 | NT | 96.6% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1299498 | 1 (0.010) | 41 (0.490) | 30/500 | NT | 98.8% | 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 | 1309390 = | 72 (0.850) | 14 (0.170) | 14/508 | NT | 16.3% | coding (880/1254 nt) | kch | voltage‑gated potassium channel |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 1568904 = | 65 (0.770) | 3 (0.040) | 3/486 | NT | 4.9% | intergenic (‑81/+50) | yddW/gadC | liprotein, glycosyl hydrolase homolog/glutamate:gamma‑aminobutyric acid antiporter |
| ? | NC_000913 | 1568931 = | 55 (0.680) | intergenic (‑108/+23) | yddW/gadC | liprotein, glycosyl hydrolase homolog/glutamate:gamma‑aminobutyric acid antiporter | |||||
| * | ? | NC_000913 | = 1612087 | 103 (1.220) | 4 (0.050) | 4/492 | NT | 3.8% | coding (239/360 nt) | yneG | DUF4186 family protein |
| ? | NC_000913 | = 1612092 | 103 (1.260) | coding (234/360 nt) | yneG | DUF4186 family protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 42 (0.500) | 30/508 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 60 (0.710) | 43/508 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | 2514275 = | NA (NA) | 3 (0.040) | 3/500 | NT | 6.9% | intergenic (+33/‑54) | nupC/insL1 | nucleoside (except guanosine) transporter/IS186 transposase |
| ? | NC_000913 | 4606214 = | 41 (0.490) | noncoding (74/87 nt) | leuP | tRNA‑Leu | |||||
| * | ? | NC_000913 | = 3169152 | 65 (0.770) | 4 (0.050) | 3/492 | NT | 5.5% | coding (78/483 nt) | ygiV | transcriptional repressor for mcbR biofilm gene |
| ? | NC_000913 | = 3169348 | 75 (0.920) | coding (327/393 nt) | ygiW | hydrogen peroxide and cadmium resistance periplasmic protein, stress‑induced OB‑fold protein | |||||
| * | ? | NC_000913 | = 4185297 | 134 (1.590) | 4 (0.050) | 4/500 | NT | 2.9% | intergenic (+25/‑52) | rpoB/rpoC | RNA polymerase, beta subunit/RNA polymerase, beta prime subunit |
| ? | NC_000913 | = 4185313 | 133 (1.600) | intergenic (+41/‑36) | rpoB/rpoC | RNA polymerase, beta subunit/RNA polymerase, beta prime subunit | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 13 (0.180) | 4/430 | NT | NA | intergenic (+38/+606) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| ? | NC_000913 | = 4296395 | NA (NA) | noncoding (562/602 nt) | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | |||||
| * | ? | NC_000913 | = 4542691 | 16 (0.190) | 3 (0.040) | 3/490 | NT | 9.3% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542987 | 43 (0.530) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||