mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 66,691 | C→T | 5.8% | intergenic (‑141/+144) | araD ← / ← araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 619,419 | G→A | 5.3% | L261F (CTC→TTC) | fepC ← | ferrienterobactin ABC transporter 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 |
| RA | 1,547,552 | Δ1 bp | 5.2% | coding (152/3048 nt) | fdnG → | formate dehydrogenase‑N, alpha subunit, nitrate‑inducible |
| RA | 1,724,800 | A→G | 6.1% | L278P (CTG→CCG) | ydhF ← | putative oxidoreductase |
| JC JC | 1,937,136 | IS2 (–) +5 bp | 100% | coding (485‑489/870 nt) | yebK → | putative DNA‑binding transcriptional regulator |
| 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 | 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 |
| JC JC | 4,049,913 | IS2 (–) +5 bp | 100% | noncoding (15‑19/109 nt) | spf → | Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,186,086 | C→A | 100% | P246Q (CCG→CAG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,060 | C→T | 20.6% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 20.7% | intergenic (+474/+168) | 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 | 583093 | 584689 | 1597 | 30 [28] | [28] 37 | [tfaX]–[ompT] | [tfaX],appY,[ompT] |
| * | * | ÷ | NC_000913 | 720832 | 721152 | 321 | 31 [29] | [29] 31 | [ybfK]–[kdpE] | [ybfK],[kdpE] |
| * | * | ÷ | NC_000913 | 1211649 | 1212801 | 1153 | 30 [28] | [29] 30 | iraM–[ycgX] | iraM,[ycgX] |
| * | * | ÷ | NC_000913 | 1299473 | 1300758 | 1286 | 30 [27] | [28] 30 | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 1465080 | 1465326 | 247 | 30 [28] | [27] 30 | ynbG | ynbG |
| * | * | ÷ | NC_000913 | 1529963 | 1530438 | 476 | 31 [28] | [27] 30 | [ydcD] | [ydcD] |
| * | * | ÷ | NC_000913 | 2470046 | 2470615 | 570 | 30 [28] | [29] 30 | [gtrS] | [gtrS] |
| * | * | ÷ | NC_000913 | 2994996 | 2995651 | 656 | 31 [29] | [27] 30 | [ygeK]–[ygeN] | [ygeK],[ygeN] |
| * | * | ÷ | NC_000913 | 3423890–3424232 | 3424400–3424242 | 11–511 | 30 [29] | [29] 30 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 3769496 | 3770239 | 744 | 30 [27] | [29] 30 | [yibV]–yibU | [yibV],yibV,yibU,yibU |
| * | * | ÷ | NC_000913 | 3798769 | 3799692 | 924 | 32 [26] | [28] 30 | [waaU]–[waaZ] | [waaU],[waaZ] |
| * | * | ÷ | NC_000913 | 4233641 | 4235885 | 2245 | 32 [25] | [28] 30 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 315229 = | NA (NA) | 4 (0.050) +TC |
4/510 | NT | 5.3% | noncoding (1/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 2157512 | 72 (0.860) | coding (2250/3123 nt) | mdtB | multidrug efflux system, subunit B | |||||
| * | ? | NC_000913 | 1207790 = | 36 (0.430) | 46 (0.580) | 40/482 | NT | 55.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 39 (0.500) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 34 (0.400) | 63 (0.800) | 43/482 | NT | 64.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 39 (0.500) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 24 (0.290) | 20/506 | 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 | 1411899 = | 83 (0.990) | 4 (0.050) | 4/462 | NT | 7.0% | coding (50/936 nt) | ttcA | tRNA s(2)C32 thioltransferase, iron sulfur cluster protein |
| ? | NC_000913 | = 1434958 | 32 (0.420) | pseudogene (51/51 nt) | ttcC | pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1650843 = | NA (NA) | 4 (0.050) +CCCGACGATAACCATACGT |
3/476 | NT | NA | noncoding (1/706 nt) | IS2 | repeat region |
| ? | NC_000913 | 1650990 = | NA (NA) | noncoding (148/706 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 28 (0.340) | 26/498 | 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 | 3156579 = | 77 (0.920) | 4 (0.050) | 4/492 | NT | 5.5% | intergenic (+61/‑44) | yqhD/dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| ? | NC_000913 | 3156603 = | 63 (0.780) | intergenic (+85/‑20) | yqhD/dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A | |||||
| * | ? | NC_000913 | 3652036 = | NA (NA) | 6 (0.070) | 6/514 | NT | 25.0% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 4049891 = | 18 (0.210) | intergenic (+139/‑8) | 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 | |||||