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 |
| 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 |
| JC | 1,157,972 | Δ60 bp | 6.4% | coding (104‑163/1434 nt) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,158,559 | C→T | 58.5% | Q231* (CAG→TAG) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,197,502 | C→T | 100% | G11R (GGA→AGA) | ymfD ← | e14 prophage; putative SAM‑dependent methyltransferase |
| RA | 1,269,726 | C→T | 12.2% | G29S (GGC→AGC) | ldrB ← | toxic polypeptide, small |
| RA | 1,466,438 | T→G | 18.9% | pseudogene (1047/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,544,021:1 | +A | 76.3% | 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 | 2,310,893 | C→T | 18.8% | A214A (GCG→GCA) | apbE ← | putative thiamine‑synthetic flavin transferase lipoprotein |
| RA | 2,418,678 | G→A | 7.8% | R167C (CGC→TGC) | yfcD ← | putative NUDIX hydrolase |
| 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 | 2,939,243 | C→T | 7.5% | A119V (GCG→GTG) | fucU → | L‑fucose mutarotase |
| RA | 3,202,613 | G→T | 7.3% | M241I (ATG→ATT) | cca → | fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and 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 | 4,296,042 | C→T | 24.8% | 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 | 4,604,698 | 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 | 365799 | 366445 | 647 | 20 [18] | [18] 19 | [lacZ]–[lacI] | [lacZ],[lacI] |
| * | * | ÷ | NC_000913_3_hsa_tpiA | 3423741–3424556 | 3424556 | 1–816 | 20 [17] | [18] 20 | [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 | = 839230 | 46 (1.030) | 3 (0.070) | 3/260 | NT | 6.3% | intergenic (‑23/+19) | ybiX/fiu | Fe(II)‑dependent oxygenase superfamily protein/catecholate siderophore receptor |
| ? | NC_000913_3_hsa_tpiA | = 839234 | 45 (1.060) | intergenic (‑27/+15) | ybiX/fiu | Fe(II)‑dependent oxygenase superfamily protein/catecholate siderophore receptor | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 1070072 | 40 (0.900) | 3 (0.070) | 3/256 | NT | 7.1% | coding (283/495 nt) | rutF | flavin:NADH reductase |
| ? | NC_000913_3_hsa_tpiA | = 1070090 | 41 (0.980) | coding (265/495 nt) | rutF | flavin:NADH reductase | |||||
| * | ? | NC_000913_3_hsa_tpiA | 1207790 = | 19 (0.430) | 28 (0.710) | 27/242 | NT | 54.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_tpiA | 1209619 = | 31 (0.790) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 1207805 | 20 (0.450) | 13 (0.330) | 13/242 | NT | 34.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_tpiA | = 1209602 | 31 (0.790) | 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) | 41 (0.950) | 34/266 | 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 | = 2601467 | 52 (1.170) | 3 (0.070) | 3/260 | NT | 5.3% | coding (267/618 nt) | hyfA | hydrogenase 4, 4Fe‑4S subunit |
| ? | NC_000913_3_hsa_tpiA | = 2601482 | 58 (1.370) | coding (282/618 nt) | hyfA | hydrogenase 4, 4Fe‑4S subunit | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 3468761 | 41 (0.920) | 4 (0.090) | 3/270 | NT | 8.5% | coding (1093/2694 nt) | chiA | periplasmic endochitinase |
| ? | NC_000913_3_hsa_tpiA | 3469086 = | 46 (1.050) | coding (768/2694 nt) | chiA | periplasmic endochitinase | |||||