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] | |
| 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 | 1,756,445 | 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 | 2,907,364 | 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 | 3,554,342 | C→T | Q420* (CAA→TAA) | malT → | mal regulon transcriptional activator |
| 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 | 4,296,381 | +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 | 1896925 | 1898281 | 1357 | 7 [6] | [0] 10 | [sdaA] | [sdaA] |
| * | * | ÷ | NC_000913 | 2684266 | 2685513 | 1248 | 8 [6] | [5] 7 | [glyA] | [glyA] |
| * | * | ÷ | NC_000913 | 2929579 | 2930928 | 1350 | 13 [0] | [0] 7 | sdaB | L‑serine dehydratase 2 |
| * | * | ÷ | NC_000913 | 3258300 | 3259649 | 1350 | 11 [0] | [6] 7 | tdcG | L‑serine dehydratase 3, anaerobic |
| * | * | ÷ | NC_000913 | 3423789–3424233 | 3424514–3424238 | 6–726 | 7 [6] | [6] 9 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4392390 | 4392588 | 199 | 7 [5] | [6] 9 | [glyV]–[glyY] | [glyV], glyX, [glyY] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 228016 = | NA (NA) | 10 (0.260) | 9/284 | 1.9 | 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 | = 282512 | 24 (0.590) | 7 (0.180) | 5/282 | 2.9 | 21.3% | coding (235/909 nt) | yagE | 2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage |
| ? | NC_000913 | = 282518 | 29 (0.750) | coding (241/909 nt) | yagE | 2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage | |||||
| * | ? | NC_000913 | 315229 = | NA (NA) | 8 (0.200) +TCA |
6/292 | 2.7 | NA | noncoding (1/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 391706 = | NA (NA) | pseudogene (1456/1458 nt) | yaiT | pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein | |||||
| * | ? | NC_000913 | 353266 = | 32 (0.790) | 6 (0.160) | 6/274 | 2.5 | 22.1% | coding (561/1887 nt) | prpE | propionate‑‑CoA ligase |
| ? | NC_000913 | 353394 = | 13 (0.350) | coding (689/1887 nt) | prpE | propionate‑‑CoA ligase | |||||
| * | ? | NC_000913 | 381292 = | NA (NA) | 5 (0.130) | 5/280 | 2.9 | 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) | 12 (0.310) | 8/280 | 2.1 | NA | noncoding (430/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381743 | NA (NA) | noncoding (484/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 1082873 | 30 (0.740) | 8 (0.210) | 8/278 | 2.1 | 23.2% | coding (631/1128 nt) | efeO | inactive ferrous ion transporter EfeUOB |
| ? | NC_000913 | = 1083021 | 25 (0.660) | coding (779/1128 nt) | efeO | inactive ferrous ion transporter EfeUOB | |||||
| * | ? | NC_000913 | 1207790 = | 16 (0.390) | 29 (0.800) | 23/266 | 0.4 | 66.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 15 (0.410) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 16 (0.390) | 21 (0.580) | 17/266 | 0.7 | 58.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 15 (0.410) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1619859 = | 33 (0.810) | 15 (0.370) | 15/298 | 1.1 | 30.9% | coding (286/384 nt) | marA | multiple antibiotic resistance transcriptional regulator |
| ? | NC_000913 | = 1623531 | 34 (0.830) | coding (320/891 nt) | dgcZ | diguanylate cyclase, zinc‑sensing | |||||
| * | ? | NC_000913 | = 3619291 | 35 (0.860) | 12 (0.320) | 6/276 | 2.6 | 27.0% | coding (100/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | = 3619450 | NA (NA) | coding (259/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 3619878 = | NA (NA) | 5 (0.130) | 5/280 | 2.9 | 100% | coding (687/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3619892 = | 0 (0.000) | coding (701/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 3927418 = | 37 (0.910) | 8 (0.210) | 7/274 | 2.3 | 21.3% | coding (264/993 nt) | asnA | asparagine synthetase A |
| ? | NC_000913 | 3927457 = | 25 (0.670) | coding (303/993 nt) | asnA | asparagine synthetase A | |||||
| * | ? | NC_000913 | 4409174 = | NA (NA) | 10 (0.270) | 9/268 | 1.8 | 20.0% | 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 = | 40 (1.090) | 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 | |||||
| * | ? | NC_000913 | 4498181 = | NA (NA) | 33 (0.810) | 8/298 | 2.3 | NA | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 4499512 | NA (NA) | intergenic (+12/+81) | insD1/yjgX | IS2 transposase TnpB/pseudogene fragment | |||||