mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| RA | 1,065,278 | C→T | R415C (CGT→TGT) | yccE → | uncharacterized protein YccE |
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| RA | 1,301,998 | A→G | S273G (AGC→GGC) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| MC JC | 1,397,239 | Δ7,315 bp | IS5‑mediated | ynaJ–[abgA] | ynaJ, uspE, fnr, ogt, abgT, abgB, [abgA] |
| MC JC | 1,411,925 | Δ23,060 bp | [ttcA]–ynaM | 34 genes [ttcA], intR, xisR, rcbA, ralA, ralR, recT, recE, racC, ydaE, kilR, kilS, sieB, ydaF, ydaG, racR, ydaS, ydaT, ydaU, ydaV, ydaW, rzoR, trkG, ynaK, ydaY, ynaA, lomR, insH5, lomR, stfR, tfaR, pinR, ynaE, ynaM |
|
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,737,584 | A→G | intergenic (‑39/‑260) | cydH ← / → purR | cytochrome bd‑I accessory subunit CydH/DNA‑binding transcriptional repressor PurR |
| RA | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC JC | 2,406,780 | IS1 (–) +8 bp | intergenic (‑139/‑774) | lrhA ← / → alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| RA | 2,867,453 | C→A | Q33Y (CAG→TAT) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,867,455 | G→A | Q33Y (CAG→TAT) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,908,319 | C→G | D450H (GAC→CAC) | pyrG ← | CTP synthetase |
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| JC JC | 3,890,892 | IS1 (+) +9 bp | coding (657‑665/1248 nt) | tnaB → | tryptophan:H(+) symporter TnaB |
| RA | 3,980,226 | G→A | V91I (GTT→ATT) | rffM → | UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| JC JC | 4,366,110 | IS1 (+) +8 bp | coding (657‑664/1302 nt) | dcuA ← | C4‑dicarboxylate transporter DcuA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1978495 | 1979270 | 776 | 142 [0] | [0] 170 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423807–3424231 | 3424486–3424238 | 8–680 | 39 [36] | [38] 39 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 66 (0.610) | 50 (0.490) | 40/566 | 1.6 | 40.9% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 82 (0.800) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 68 (0.620) | 53 (0.510) | 46/566 | 1.1 | 42.0% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 82 (0.800) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299498 | 1 (0.010) | 133 (1.270) | 85/574 | 0.1 | 99.2% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | = 1300693 | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1299499 = | NA (NA) | 133 (1.270) | 81/574 | 0.1 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1300694 = | 0 (0.000) | intergenic (+147/‑488) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 141 (1.290) | 83/598 | 0.1 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 169 (1.550) | 102/598 | 0.0 | 100% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||