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 | 1,405 | A→C | S357R (AGC→CGC) | thrA → | Bifunctional aspartokinase/homoserine dehydrogenase 1 |
| JC JC | 121,518 | IS5 (+) +4 bp | coding (31‑34/1374 nt) | aroP ← | aromatic amino acid transporter |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 1,756,445 | G→T | E250* (GAA→TAA) | pykF → | pyruvate kinase I |
| 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 | 2,025,007 | A→C | S8R (AGC→CGC) | yodD → | uncharacterized 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 |
| RA | 2,599,861 | (T)8→7 | intergenic (‑101/‑45) | dapA ← / → gcvR | dihydrodipicolinate synthase/transcriptional repressor, regulatory protein accessory to GcvA |
| RA | 2,815,907 | G→A | A178V (GCG→GTG) | gshA ← | glutamate‑cysteine ligase |
| RA | 2,907,364 | A→T | L193Q (CTG→CAG) | eno ← | enolase |
| JC JC | 2,942,878 | IS4 (+) +13 bp | intergenic (‑311/+28) | gcvA ← / ← ygdI | glycine cleavage system transcriptional activator; autorepressor/DUF903 family verified lipoprotein |
| 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 | 4,182,803 | C→T | P520L (CCG→CTG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,248,304 | C→T | Q112* (CAG→TAG) | lamB → | maltose outer membrane porin (maltoporin) |
| 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 | 1896933 | 1898281 | 1349 | 10 [9] | [0] 20 | sdaA | L‑serine dehydratase 1 |
| * | * | ÷ | NC_000913 | 2684250 | 2685529 | 1280 | 10 [9] | [9] 10 | glyA | glyA |
| * | * | ÷ | NC_000913 | 2929578 | 2930945 | 1368 | 11 [8] | [9] 10 | [sdaB] | [sdaB] |
| * | * | ÷ | NC_000913 | 3258300 | 3259646 | 1347 | 10 [0] | [0] 17 | tdcG | L‑serine dehydratase 3, anaerobic |
| * | * | ÷ | NC_000913 | 3423785–3424233 | 3424514–3424239 | 7–730 | 13 [7] | [7] 11 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381258 = | NA (NA) | 215 (3.960) | 52/294 | 0.0 | NA | pseudogene (3/417 nt) | yaiX | pseudogene, interrupted by IS2A; hexapeptide transferase superfamily; putative transferase |
| ? | NC_000913 | = 382589 | NA (NA) | noncoding (1330/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 381292 = | NA (NA) | 17 (0.330) | 12/278 | 1.9 | NA | noncoding (33/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381312 = | NA (NA) | noncoding (53/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 381689 | NA (NA) | 9 (0.180) | 8/278 | 2.8 | NA | noncoding (430/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381743 | NA (NA) | noncoding (484/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 34 (0.620) | 19 (0.390) | 17/264 | 1.1 | 35.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 38 (0.780) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 34 (0.620) | 18 (0.370) | 15/264 | 1.3 | 34.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 38 (0.780) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1242815 = | 31 (0.570) | 8 (0.150) | 8/280 | 2.8 | 22.4% | coding (266/915 nt) | ldcA | murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A |
| ? | NC_000913 | 1242848 = | 26 (0.500) | coding (233/915 nt) | ldcA | murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 60 (1.130) | 45/288 | 0.0 | 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 | 1590765 = | 53 (0.970) | 462 (8.760) | 141/286 | 0.0 | 90.9% | intergenic (‑229/+89) | yneL/hipA | pseudogene, AraC family/inactivating GltX kinase facilitating persister formation; toxin of HipAB TA pair; autokinase |
| ? | NC_000913 | = 1647024 | 41 (0.780) | intergenic (+287/+150) | flxA/intK | Qin prophage; uncharacterized protein/pseudogene, integrase fragment, Qin prophage;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1619859 = | 481 (8.810) | 4422 (80.950) | 244/296 | 0.0 | 90.2% | coding (286/384 nt) | marA | multiple antibiotic resistance transcriptional regulator |
| ? | NC_000913 | = 1623531 | 474 (8.680) | coding (320/891 nt) | dgcZ | diguanylate cyclase, zinc‑sensing | |||||
| * | ? | NC_000913 | 4409174 = | NA (NA) | 11 (0.220) | 7/266 | 2.9 | 22.4% | noncoding (22/98 nt) | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 4409235 = | 38 (0.770) | noncoding (83/98 nt) | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||