mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 61,802 | T→G | 6.8% | D488A (GAT→GCT) | rapA ← | RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase |
| JC | 62,752 | +GGCGCGT | 10.2% | coding (513/2907 nt) | rapA ← | RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| 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 | 526,982 | A→T | 6.5% | N1241I (AAT→ATT) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 1,196,305 | C→T | 100% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,273,648 | Δ1 bp | 5.3% | intergenic (‑49/‑136) | ychN ← / → ychO | putative sulfur relay protein/putative invasin |
| 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 | 1,411,925 | 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 | 1,675,664 | Δ6 bp | 26.9% | coding (692‑697/1389 nt) | pntB ← | pyridine nucleotide transhydrogenase, beta subunit |
| RA | 1,750,268 | C→T | 6.4% | P27P (CCG→CCA) | ydhU ← | putative cytochrome b subunit of YdhYVWXUT oxidoreductase complex |
| RA | 1,950,587 | Δ1 bp | 5.1% | intergenic (‑65/‑245) | aspS ← / → yecD | aspartyl‑tRNA synthetase/isochorismatase family protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | 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 | 2,173,361 | 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 | 2,233,949 | C→T | 9.1% | intergenic (+110/‑84) | yeiS → / → preT | DUF2542 family protein/dihydropyrimidine dehydrogenase, NADH‑dependent, subunit N |
| RA | 2,468,903 | Δ1 bp | 8.9% | coding (690/921 nt) | gtrB → | CPS‑53 (KpLE1) prophage; bactoprenol glucosyl transferase |
| RA | 3,214,415 | A→C | 100% | I457L (ATT→CTT) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| 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 | 4,049,886 | 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 | 4,160,854 | C→T | 48.4% | intergenic (‑64/‑270) | sthA ← / → fabR | pyridine nucleotide transhydrogenase, soluble/transcriptional repressor of fabA and fabB |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,190 | A→G | 15.7% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 16.2% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 31.9% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 18.4% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 11.7% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 10.4% | 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 | 3423870–3424232 | 3424403–3424239 | 8–534 | 25 [24] | [24] 28 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4233737 | 4235504 | 1768 | 27 [24] | [23] 25 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 762116 = | 101 (1.210) | 8 (0.100) | 4/480 | NT | 7.2% | coding (595/1218 nt) | sucB | dihydrolipoyltranssuccinase |
| ? | NC_000913 | 762340 = | 110 (1.390) | coding (819/1218 nt) | sucB | dihydrolipoyltranssuccinase | |||||
| * | ? | NC_000913 | 1207790 = | 33 (0.390) | 24 (0.310) | 23/476 | NT | 46.6% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 24 (0.310) | 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 (0.310) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 1 (0.010) | 41 (0.500) | 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 (0.860) | 14 (0.170) | 14/508 | NT | 16.3% | coding (880/1254 nt) | kch | voltage‑gated potassium channel |
| ? | NC_000913 | = 1979270 | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 2514273 = | NA (NA) | 3 (0.040) | 3/500 | NT | 7.5% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 4606217 = | 37 (0.450) | noncoding (70/87 nt) | leuP | tRNA‑Leu | |||||
| * | ? | NC_000913 | = 3169154 | 65 (0.780) | 4 (0.050) | 3/492 | NT | 5.5% | coding (78/483 nt) | ygiV | transcriptional repressor for mcbR biofilm gene |
| ? | NC_000913 | = 3169350 | 74 (0.910) | coding (327/393 nt) | ygiW | hydrogen peroxide and cadmium resistance periplasmic protein; stress‑induced OB‑fold protein | |||||
| * | ? | NC_000913 | = 4542690 | 16 (0.190) | 3 (0.040) | 3/490 | NT | 9.5% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 42 (0.520) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||