mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 195,316 | G→A | 9.0% | T138T (ACG→ACA) | ispU → | undecaprenyl pyrophosphate synthase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 264,098 | G→T | 100% | L50L (CTC→CTA) | ykfH ← | uncharacterized protein |
| RA | 275,065 | G→A | 100% | T18I (ACC→ATC) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 389,919:1 | +T | 100% | intergenic (‑192/‑332) | hemB ← / → yaiT | 5‑aminolevulinate dehydratase (porphobilinogen synthase)/pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein |
| RA | 482,230 | G→A | 100% | P725L (CCG→CTG) | acrB ← | multidrug efflux system protein |
| RA | 1,197,502 | C→T | 100% | G11R (GGA→AGA) | ymfD ← | e14 prophage; putative SAM‑dependent methyltransferase |
| RA | 1,544,021:1 | +A | 68.0% | coding (40/1389 nt) | narU ← | nitrate/nitrite transporter |
| RA | 1,544,022 | C→A | 100% | L13F (TTG→TTT) | narU ← | nitrate/nitrite transporter |
| RA | 1,774,576 | G→A | 100% | G263E (GGG→GAG) | ydiB → | quinate/shikimate 5‑dehydrogenase, NAD(P)‑binding |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,106,741 | A→T | 100% | S162S (TCT→TCA) | wbbH ← | O‑antigen polymerase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,679,525 | G→T | 100% | A1074D (GCT→GAT) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,795,396 | C→A | 100% | Q382K (CAG→AAG) | gabP → | gamma‑aminobutyrate transporter |
| RA | 2,817,170 | C→A | 100% | E112* (GAA→TAA) | yqaB ← | fructose‑1‑P and 6‑phosphogluconate phosphatase |
| RA | 3,560,455:1 | +G | 100% | 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 | 3,793,162 | G→T | 17.6% | F174L (TTC→TTA) | yibB ← | YibB family protein, function unknown |
| RA | 3,903,015 | C→A | 23.5% | G229G (GGG→GGT) | bglB ← | cryptic phospho‑beta‑glucosidase B |
| RA | 4,296,042 | C→T | 19.6% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,362:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,332,850 | G→T | 8.6% | R135R (CGC→CGA) | basS ← | sensory histidine kinase in two‑component regulatory system with BasR |
| RA | 4,604,698 | C→A | 100% | A186E (GCA→GAA) | bglJ → | bgl operon transcriptional activator |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913_3_hsa_tpiA | 365922 | 366442 | 521 | 14 [13] | [13] 14 | [lacZ]–[lacI] | [lacZ],[lacI] |
| * | * | ÷ | NC_000913_3_hsa_tpiA | 3423760–3424552 | 3424552 | 1–793 | 16 [12] | [13] 14 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_hsa_tpiA | 1207790 = | 17 (0.470) | 26 (0.810) | 23/244 | NT | 59.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_tpiA | 1209619 = | 20 (0.620) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 1207805 | 19 (0.520) | 14 (0.440) | 14/244 | NT | 43.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_tpiA | = 1209602 | 20 (0.620) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 1299498 | 0 (0.000) | 46 (1.300) | 39/268 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913_3_hsa_tpiA | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 1498531 | 23 (0.630) | 3 (0.090) | 3/260 | NT | 12.1% | intergenic (+20/‑120) | opgD/ydcH | OPG biosynthetic periplasmic protein/DUF465 family protein |
| ? | NC_000913_3_hsa_tpiA | = 1498539 | 22 (0.640) | intergenic (+28/‑112) | opgD/ydcH | OPG biosynthetic periplasmic protein/DUF465 family protein | |||||
| * | ? | NC_000913_3_hsa_tpiA | 2729443 = | 23 (0.630) | 3 (0.090) | 3/256 | NT | 12.4% | noncoding (2/76 nt) | gltW | tRNA‑Glu |
| ? | NC_000913_3_hsa_tpiA | 2729485 = | 21 (0.620) | intergenic (‑41/+131) | gltW/rrsG | tRNA‑Glu/16S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913_3_hsa_tpiA | 3767207 = | 29 (0.800) | 3 (0.080) | 3/268 | NT | 9.2% | intergenic (+28/‑14) | yibA/rhsJ | putative immunity protein for polymorphic toxin RhsA; HEAT‑domain protein; lethality reduction protein/Rhs‑family protein |
| ? | NC_000913_3_hsa_tpiA | 3767245 = | 31 (0.880) | pseudogene (25/945 nt) | rhsJ | Rhs‑family protein | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 4124692 | 39 (1.070) | 3 (0.080) | 3/276 | NT | 7.1% | coding (2101/2199 nt) | priA | Primosome factor n' (replication factor Y) |
| ? | NC_000913_3_hsa_tpiA | = 4124710 | 39 (1.070) | coding (2083/2199 nt) | priA | Primosome factor n' (replication factor Y) | |||||