mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.29.0 revision 8f9c342918e4
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 | [crl] | [crl] | |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| JC JC | 2,628,616 | IS2 (+) +5 bp | coding (319‑323/2244 nt) | yfgF ← | cyclic‑di‑GMP phosphodiesterase, anaerobic |
| RA | 2,780,609 | A→C | G706G (GGT→GGG) | ypjA ← | adhesin‑like autotransporter |
| RA | 3,440,194 | C→A | G279V (GGT→GTT) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,560,455 | +G | 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 | 4,161,155 | C→A | T11N (ACC→AAC) | fabR → | transcriptional repressor of fabA and fabB |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | 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 | 583371 | 584809 | 1439 | 11 [10] | [10] 12 | appY–[ompT] | appY, [ompT] |
| * | * | ÷ | NC_000913 | 1216470 | 1216789 | 320 | 11 [10] | [10] 11 | [ariR]–[ymgC] | [ariR], [ymgC] |
| * | * | ÷ | NC_000913 | 1978503 | 1979298 | 796 | 11 [0] | [10] 11 | insB1–insA | insB1, insA |
| * | * | ÷ | NC_000913 | 2786209 | 2788529 | 2321 | 11 [10] | [10] 11 | [ygaQ] | [ygaQ] |
| * | * | ÷ | NC_000913 | 2987112 | 2992439 | 5328 | 11 [10] | [10] 11 | yqeH–[ygeH] | yqeH, yqeI, yqeJ, yqeL, yqeK, ygeF, ygeF, ygeG, [ygeH] |
| * | * | ÷ | NC_000913 | 3423783–3424232 | 3424557–3424239 | 8–775 | 11 [9] | [10] 11 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 3632680 | 3634444 | 1765 | 11 [10] | [10] 11 | yhiL–[yhiL] | yhiL, [yhiL] |
| * | * | ÷ | NC_000913 | 3767936 | 3769017 | 1082 | 11 [10] | [10] 11 | [rhsJ]–[yibW] | [rhsJ], yibG, yibS, yibW, [yibW] |
| * | * | ÷ | NC_000913 | 3803949 | 3805288 | 1340 | 11 [10] | [10] 11 | [waaB]–[waaP] | [waaB], waaS, [waaP] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1207805 | 18 (0.510) | 9 (0.290) | 8/260 | 2.8 | 31.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 24 (0.770) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 16 (0.470) | 15/284 | 1.6 | 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 | = 1978502 | 0 (0.000) | 10 (0.300) | 10/276 | 2.5 | 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 | 2347159 = | NA (NA) | 31 (0.920) +CCCGGA |
17/280 | 1.2 | NA | intergenic (+9/‑225) | nrdA/nrdB | ribonucleoside‑diphosphate reductase 1, alpha subunit/ribonucleoside‑diphosphate reductase 1, beta subunit, ferritin‑like protein |
| ? | NC_000913 | = 2431012 | NA (NA) | noncoding (84/84 nt) | REP169 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP169 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||