Search for Variation information by Variation ID:
Detailed information for vg0714148441:
| Variant ID: vg0714148441 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14148441 |
| Reference Allele: A | Alternative Allele: G,T |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AAAGGGTGTCTTCGTTTGATAGGAGGATGCTAGGGTCAACCGTCACCGTGAAAGGGGGTTGCCCATCAAACTGATCATAATCCTCGTCAGTCTTGTCCTC[A/G,T]
ACTCCGATGATTTTTCTTTTGCTAGGGAGAACCACGTGGCACTTCGGCTCATCAGGCCCTTTGCCCTTCTTTCCTTTGCTAGACATGTCCTTCACATAAA
Reverse complement sequence
TTTATGTGAAGGACATGTCTAGCAAAGGAAAGAAGGGCAAAGGGCCTGATGAGCCGAAGTGCCACGTGGTTCTCCCTAGCAAAAGAAAAATCATCGGAGT[T/C,A]
GAGGACAAGACTGACGAGGATTATGATCAGTTTGATGGGCAACCCCCTTTCACGGTGACGGTTGACCCTAGCATCCTCCTATCAAACGAAGACACCCTTT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 45.40% | 8.40% | 14.49% | 31.55% | T: 0.08% |
| All Indica | 2759 | 26.70% | 11.70% | 18.05% | 43.42% | T: 0.11% |
| All Japonica | 1512 | 83.30% | 0.40% | 1.52% | 14.81% | NA |
| Aus | 269 | 36.40% | 20.40% | 34.57% | 8.55% | NA |
| Indica I | 595 | 51.30% | 2.90% | 8.91% | 36.97% | NA |
| Indica II | 465 | 25.80% | 9.70% | 12.90% | 51.61% | NA |
| Indica III | 913 | 7.80% | 18.70% | 26.07% | 47.21% | T: 0.22% |
| Indica Intermediate | 786 | 30.70% | 11.50% | 18.70% | 39.06% | T: 0.13% |
| Temperate Japonica | 767 | 84.50% | 0.30% | 1.04% | 14.21% | NA |
| Tropical Japonica | 504 | 93.80% | 0.20% | 0.99% | 4.96% | NA |
| Japonica Intermediate | 241 | 57.30% | 1.20% | 4.15% | 37.34% | NA |
| VI/Aromatic | 96 | 9.40% | 12.50% | 58.33% | 18.75% | T: 1.04% |
| Intermediate | 90 | 48.90% | 3.30% | 16.67% | 31.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0714148441 | A -> DEL | LOC_Os07g24880.1 | N | frameshift_variant | Average:6.25; most accessible tissue: Callus, score: 15.854 | N | N | N | N |
| vg0714148441 | A -> G | LOC_Os07g24880.1 | synonymous_variant ; p.Val378Val; LOW | synonymous_codon | Average:6.25; most accessible tissue: Callus, score: 15.854 | N | N | N | N |
| vg0714148441 | A -> G | LOC_Os07g24880.1 | synonymous_variant ; p.Val378Val; LOW | nonsynonymous_codon ; V378I | Average:6.25; most accessible tissue: Callus, score: 15.854 | benign  |
0.482 |
DELETERIOUS | 0.00 |
| vg0714148441 | A -> T | LOC_Os07g24880.1 | synonymous_variant ; p.Val378Val; LOW | synonymous_codon | Average:6.25; most accessible tissue: Callus, score: 15.854 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714148441 | NA | 1.07E-06 | mr1063 | Jap_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0714148441 | NA | 3.82E-07 | mr1405 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0714148441 | NA | 4.77E-06 | mr1532 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0714148441 | NA | 2.61E-06 | mr1574_2 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |