Search for Variation information by Variation ID:
Detailed information for vg0716085277:
| Variant ID: vg0716085277 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 16085277 |
| Reference Allele: A | Alternative Allele: G,C |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, C: 0.20, A: 0.04, others allele: 0.00, population size: 94. )
Flanking Sequence (100 bp) in Reference Genome:
TTCGGCGCTTTAATGAGTGCAGAAATACAATCCCTGAAATCACCGACGCTTCTGTAATCCGCGCTTTCAAGTCCAGTGTCAGAGATCGCTATACTACCCA[A/G,C]
GAGTTGGCAACGAGGCGCATCACGACTACTCGGAGATTATTCGAGATTGTCGATCGATGCGCCCACGCGGACGACGTACTGAGACGCAAGAACGACAAGC
Reverse complement sequence
GCTTGTCGTTCTTGCGTCTCAGTACGTCGTCCGCGTGGGCGCATCGATCGACAATCTCGAATAATCTCCGAGTAGTCGTGATGCGCCTCGTTGCCAACTC[T/C,G]
TGGGTAGTATAGCGATCTCTGACACTGGACTTGAAAGCGCGGATTACAGAAGCGTCGGTGATTTCAGGGATTGTATTTCTGCACTCATTAAAGCGCCGAA
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 | 33.70% | 29.00% | 1.18% | 35.51% | C: 0.53% |
| All Indica | 2759 | 4.10% | 40.20% | 1.78% | 53.93% | C: 0.07% |
| All Japonica | 1512 | 87.70% | 11.70% | 0.07% | 0.46% | C: 0.07% |
| Aus | 269 | 9.30% | 24.50% | 1.49% | 58.74% | C: 5.95% |
| Indica I | 595 | 4.00% | 53.10% | 1.01% | 41.85% | NA |
| Indica II | 465 | 8.00% | 16.60% | 3.01% | 72.47% | NA |
| Indica III | 913 | 1.40% | 35.30% | 1.86% | 61.34% | C: 0.11% |
| Indica Intermediate | 786 | 4.80% | 50.00% | 1.53% | 43.51% | C: 0.13% |
| Temperate Japonica | 767 | 77.80% | 21.60% | 0.00% | 0.52% | NA |
| Tropical Japonica | 504 | 98.20% | 1.60% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.10% | 1.20% | 0.00% | 1.24% | C: 0.41% |
| VI/Aromatic | 96 | 91.70% | 3.10% | 0.00% | 0.00% | C: 5.21% |
| Intermediate | 90 | 48.90% | 20.00% | 2.22% | 27.78% | C: 1.11% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0716085277 | A -> DEL | LOC_Os07g27520.1 | N | frameshift_variant | Average:14.258; most accessible tissue: Callus, score: 35.463 | N | N | N | N |
| vg0716085277 | A -> G | LOC_Os07g27520.1 | synonymous_variant ; p.Gln407Gln; LOW | nonsynonymous_codon ; Q407L | Average:14.258; most accessible tissue: Callus, score: 35.463 | benign  |
1.341 |
DELETERIOUS | 0.02 |
| vg0716085277 | A -> G | LOC_Os07g27520.1 | synonymous_variant ; p.Gln407Gln; LOW | synonymous_codon | Average:14.258; most accessible tissue: Callus, score: 35.463 | N | N | N | N |
| vg0716085277 | A -> C | LOC_Os07g27520.1 | missense_variant ; p.Gln407His; MODERATE | nonsynonymous_codon ; Q407H | Average:14.258; most accessible tissue: Callus, score: 35.463 | probably damaging |
2.213 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0716085277 | 1.14E-06 | NA | mr1091_2 | Ind_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 |
| vg0716085277 | NA | 2.66E-09 | mr1947_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 |