mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 222,965 | (A)8→7 | coding (133/576 nt) | gmhB → | D,D‑heptose 1,7‑bisphosphate phosphatase |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 494,987 | G→T | G195W (GGG→TGG) | recR → | gap repair protein |
| RA | 702,338 | (T)7→8 | coding (414/1149 nt) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 987,008 | (T)8→7 | intergenic (‑26/+577) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 1,049,313 | G→A | S7L (TCG→TTG) | gfcB ← | O‑antigen capsule production lipoprotein |
| RA | 1,351,196 | (G)7→6 | intergenic (‑157/+211) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,019,460 | G→A | V359I (GTC→ATC) | fliK → | flagellar hook‑length control protein |
| RA | 2,147,021 | T→C | M174V (ATG→GTG) | alkA ← | 3‑methyl‑adenine DNA glycosylase II |
| 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 |
| RA | 2,297,114 | (C)7→8 | coding (531/624 nt) | ccmA ← | heme export ABC transporter ATPase |
| JC JC | 2,375,828 | IS186 (+) +4 bp | coding (132‑135/963 nt) | menC ← | O‑succinylbenzoyl‑CoA synthase |
| RA | 2,471,252 | T→C | N89S (AAC→AGC) | yfdK ← | CPS‑53 (KpLE1) prophage; conserved protein |
| RA | 2,821,424 | G→C | G196G (GGC→GGG) | alaS ← | alanyl‑tRNA synthetase |
| RA | 2,859,142 | G→A | A684T (GCC→ACC) | mutS → | methyl‑directed mismatch repair protein |
| RA | 2,904,212 | G→A | intergenic (+838/+535) | ygcE → / ← queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| 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 |
| JC JC | 3,890,075 | IS5 (–) +4 bp | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 3,982,684 | (C)8→9 | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
| RA | 4,186,578 | A→G | D410G (GAT→GGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,285,364 | T→C | intergenic (‑151/+49) | yjcH ← / ← acs | DUF485 family inner membrane protein/acetyl‑CoA synthetase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,406,129 | T→C | intergenic (+144/‑61) | purA → / → nsrR | adenylosuccinate synthetase/nitric oxide‑sensitive repressor for NO regulon |
| RA | 4,606,215 | (G)8→9 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,633,657 | C→T | C30Y (TGC→TAC) | yjjX ← | non‑canonical purine NTP phosphatase, ITPase/XTPase |
| JC JC | 4,640,551 | IS1 (–) +9 bp | intergenic (+9/‑383) | yjjY → / → yjtD | uncharacterized protein/putative methyltransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 773034 | 774173 | 1140 | 28 [25] | [22] 26 | [cydB] | [cydB] |
| * | * | ÷ | NC_000913 | 1037709 | 1039287 | 1579 | 26 [25] | [25] 26 | cbdA | cbdA |
| * | * | ÷ | NC_000913 | 1166018 | 1167429 | 1412 | 26 [25] | [24] 28 | ndh | ndh |
| * | * | ÷ | NC_000913 | 3423770–3424523 | 3424523 | 1–754 | 26 [21] | [14] 27 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374930 = | NA (NA) | 31 (0.450) | 10/190 | 2.6 | 24.1% | noncoding (1/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | NC_000913 | 377522 = | 107 (1.420) | intergenic (+211/+13) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | NC_000913 | 1207790 = | 7 (0.070) | 58 (0.650) | 31/244 | 0.6 | 83.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 17 (0.190) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 7 (0.070) | 56 (0.630) | 31/244 | 0.6 | 82.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 17 (0.190) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 71 (0.730) | 42/268 | 0.3 | 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 | |||||