mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 526,792 | A→C | 24.9% | S1178R (AGC→CGC) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 526,796 | C→G | 29.9% | A1179G (GCG→GGG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 526,800 | A→G | 26.9% | E1180E (GAA→GAG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 1,466,201 | T→C | 21.4% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,527,876 | C→T | 9.8% | intergenic (+724/‑26) | yncH → / → rhsE | IPR020099 family protein/pseudogene, Rhs family |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| 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 | 2,555,718 | G→A | 9.7% | A4V (GCA→GTA) | eutK ← | putative ethanol utilization carboxysome structural protein |
| RA | 3,440,084:1 | +G | 65.2% | coding (946/990 nt) | rpoA ← | RNA polymerase, alpha subunit |
| 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 | 3,741,287 | C→T | 9.5% | C99Y (TGC→TAC) | ysaA ← | putative hydrogenase, 4Fe‑4S ferredoxin‑type component |
| RA | 4,235,433 | Δ1 bp | 100% | intergenic (‑2200/‑501) | lysC ← / → yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,296,088 | C→T | 24.1% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,408:1 | +CG | 100% | intergenic (+586/+56) | 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_3_hsa_pgi | 365878 | 366466 | 589 | 13 [12] | [12] 13 | [lacZ]–[lacI] | [lacZ],[lacI] |
| * | * | ÷ | NC_000913_3_hsa_pgi | 1528425–1529174 | 1529230–1529181 | 8–806 | 13 [12] | [12] 13 | rhsE | pseudogene, Rhs family |
| * | * | ÷ | NC_000913_3_hsa_pgi | 3423760–3424234 | 3424524–3424238 | 5–765 | 13 [12] | [12] 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_pgi | 1207790 = | 4 (0.110) | 39 (1.260) | 34/242 | NT | 87.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_pgi | 1209619 = | 8 (0.260) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_pgi | = 1207805 | 4 (0.110) | 23 (0.740) | 18/242 | NT | 80.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_pgi | = 1209602 | 8 (0.260) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_pgi | = 1299498 | 0 (0.000) | 32 (0.940) | 30/266 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913_3_hsa_pgi | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913_3_hsa_pgi | = 2024596 | 39 (1.110) | 3 (0.090) | 3/274 | NT | 7.6% | intergenic (+5/+39) | rcsA/dsrB | transcriptional regulator of colanic acid capsular biosynthesis/uncharacterized protein |
| ? | NC_000913_3_hsa_pgi | = 2024624 | 34 (0.970) | intergenic (+33/+11) | rcsA/dsrB | transcriptional regulator of colanic acid capsular biosynthesis/uncharacterized protein | |||||
| * | ? | NC_000913_3_hsa_pgi | 2362102 = | 32 (0.910) | 3 (0.090) | 3/266 | NT | 7.7% | coding (110/783 nt) | rhmR | putative DNA‑binding transcriptional regulator for the rhm operon |
| ? | NC_000913_3_hsa_pgi | 2362167 = | 41 (1.200) | coding (45/783 nt) | rhmR | putative DNA‑binding transcriptional regulator for the rhm operon | |||||