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 |
| 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 | 7 [6] | [0] 10 | [sdaA] | [sdaA] |
| * | * | ÷ | NC_000913 | 2684275 | 2685505 | 1231 | 7 [6] | [5] 7 | glyA | serine hydroxymethyltransferase |
| * | * | ÷ | NC_000913 | 2929579 | 2930928 | 1350 | 9 [0] | [0] 12 | sdaB | L‑serine dehydratase 2 |
| * | * | ÷ | NC_000913 | 3258300 | 3259646 | 1347 | 12 [0] | [0] 19 | tdcG | L‑serine dehydratase 3, anaerobic |
| * | * | ÷ | NC_000913 | 3423785–3424234 | 3424514–3424238 | 5–730 | 8 [3] | [5] 9 | [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) | 5 (0.120) | 5/284 | 2.9 | 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) | 9 (0.220) | 6/280 | 2.6 | NA | noncoding (33/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381312 = | NA (NA) | noncoding (53/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 5 (0.110) | 41 (1.050) | 30/266 | 0.1 | 92.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 2 (0.050) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 5 (0.110) | 24 (0.620) | 19/266 | 0.6 | 88.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 2 (0.050) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1285349 | 22 (0.500) | 6 (0.150) | 6/282 | 2.6 | 20.8% | coding (211/711 nt) | narJ | molybdenum‑cofactor‑assembly chaperone delta subunit of nitrate reductase 1 |
| ? | NC_000913 | = 1285396 | 25 (0.610) | coding (258/711 nt) | narJ | molybdenum‑cofactor‑assembly chaperone delta subunit of nitrate reductase 1 | |||||
| * | ? | NC_000913 | 1467909 = | NA (NA) | 19 (0.440) | 9/298 | 2.0 | NA | intergenic (+5/+12) | ydbA/insD1 | pseudogene, autotransporter homolog; interrupted by IS2 and IS30/IS2 transposase TnpB |
| ? | NC_000913 | = 1469240 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1615598 = | 49 (1.120) | 1753 (41.870) | 167/286 | 0.0 | 97.5% | coding (795/882 nt) | yneJ | putative DNA‑binding transcriptional regulator |
| ? | NC_000913 | = 1625301 | 43 (1.030) | intergenic (+10/+34) | ydeJ/dcp | inactive PncC family protein/dipeptidyl carboxypeptidase II | |||||