mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.27.1 revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 1,403 | A→G | Y356C (TAC→TGC) | thrA → | Bifunctional aspartokinase/homoserine dehydrogenase 1 |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 450,073 | C→T | W190* (TGG→TAG) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 822,421 | C→T | L26L (TTG→TTA) | ybhN ← | UPF0104 family inner membrane protein |
| RA | 933,022 | A→G | D143G (GAC→GGC) | lrp → | leucine‑responsive global transcriptional regulator |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| JC JC | 1,673,670 | IS1 (–) +9 bp | intergenic (‑169/‑235) | mdtJ ← / → tqsA | multidrug efflux system transporter/pheromone AI‑2 transporter |
| RA | 1,818,103 | A→T | V133E (GTA→GAA) | chbF ← | phospho‑chitobiase; general 6‑phospho‑beta‑glucosidase activity |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| 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 | 2,492,323 | IS1 (–) +9 bp | coding (924‑932/1251 nt) | frc ← | formyl‑CoA transferase, NAD(P)‑binding |
| RA | 2,907,364 | A→T | L193Q (CTG→CAG) | eno ← | enolase |
| RA | 2,907,452 | C→G | V164L (GTT→CTT) | eno ← | enolase |
| RA | 3,060,146 | C→A | Q132K (CAG→AAG) | argP → | transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor |
| RA | 3,471,274 | C→A | G19V (GGC→GTC) | tufA ← | translation elongation factor EF‑Tu 1 |
| 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 | 3,966,174 | IS1 (–) +9 bp | intergenic (+84/‑235) | trxA → / → rho | thioredoxin 1/transcription termination factor |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,430,521 | A→G | I220V (ATA→GTA) | cycA → | D‑alanine/D‑serine/glycine transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1896925 | 1898281 | 1357 | 8 [7] | [0] 14 | [sdaA] | [sdaA] |
| * | * | ÷ | NC_000913 | 2684266 | 2685547 | 1282 | 9 [5] | [7] 9 | [glyA] | [glyA] |
| * | * | ÷ | NC_000913 | 2929579 | 2930928 | 1350 | 13 [0] | [0] 12 | sdaB | L‑serine dehydratase 2 |
| * | * | ÷ | NC_000913 | 3258300 | 3259646 | 1347 | 11 [0] | [0] 16 | tdcG | L‑serine dehydratase 3, anaerobic |
| * | * | ÷ | NC_000913 | 3423785–3424233 | 3424513–3424239 | 7–729 | 8 [5] | [7] 8 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 228016 = | NA (NA) | 7 (0.160) | 6/282 | 2.8 | NA | noncoding (2258/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 228041 = | NA (NA) | noncoding (2283/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 381292 = | NA (NA) | 8 (0.180) | 8/278 | 2.2 | NA | noncoding (33/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381312 = | NA (NA) | noncoding (53/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 11 (0.240) | 44 (1.060) | 32/264 | 0.1 | 82.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 9 (0.220) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 11 (0.240) | 30 (0.730) | 24/264 | 0.4 | 76.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 9 (0.220) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1432648 | NA (NA) | 8 (0.180) | 6/280 | 2.8 | 26.1% | coding (238/576 nt) | tfaR | Rac prophage; putative tail fiber assembly protein |
| ? | NC_000913 | 1634576 = | 24 (0.520) | coding (310/576 nt) | tfaQ | Qin prophage; putative tail fibre assembly protein | |||||
| * | ? | NC_000913 | 1615598 = | 41 (0.880) | 2137 (48.040) | 179/284 | 0.0 | 98.4% | coding (795/882 nt) | yneJ | putative DNA‑binding transcriptional regulator |
| ? | NC_000913 | = 1625301 | 31 (0.700) | intergenic (+10/+34) | ydeJ/dcp | inactive PncC family protein/dipeptidyl carboxypeptidase II | |||||
| * | ? | NC_000913 | 3060398 = | 31 (0.670) | 8 (0.180) | 8/280 | 2.3 | 21.5% | coding (646/894 nt) | argP | transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor |
| ? | NC_000913 | 3060457 = | 29 (0.660) | coding (705/894 nt) | argP | transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor | |||||
| * | ? | NC_000913 | = 3529405 | 31 (0.670) | 8 (0.190) | 7/276 | 2.5 | 21.9% | coding (58/402 nt) | hslR | ribosome‑associated heat shock protein Hsp15 |
| ? | NC_000913 | = 3529461 | 28 (0.650) | coding (114/402 nt) | hslR | ribosome‑associated heat shock protein Hsp15 | |||||
| * | ? | NC_000913 | 3764005 = | 32 (0.690) | 11 (0.250) | 6/280 | 2.8 | 21.3% | coding (1823/4134 nt) | rhsA | Rhs protein with putative toxin 55 domain; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3764057 = | 51 (1.160) | coding (1875/4134 nt) | rhsA | Rhs protein with putative toxin 55 domain; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 4498181 = | NA (NA) | 49 (1.060) | 11/296 | 1.8 | NA | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 4499512 | NA (NA) | intergenic (+12/+81) | insD1/yjgX | IS2 transposase TnpB/pseudogene fragment | |||||