Search for Variation information by Variation ID:
Detailed information for vg0808829838:
| Variant ID: vg0808829838 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 8829838 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GAGCTGACACTCGCCCTGCAGACTCCAGAGCATCCAGGACGAACACGAGGGAAATGGGTGATTCCTTGGAAGATTGGTTTTAAGGAGGACATCCACACGT[A/C]
CAGGAGTCAGATGAGGAGCAAGAGAGATACCGAGGCGAAGATTGCAGATCTAGAGTTCCGGGTATCGAGCTACGAGCTCAGCATGCAAGAGGAGGTGGCA
Reverse complement sequence
TGCCACCTCCTCTTGCATGCTGAGCTCGTAGCTCGATACCCGGAACTCTAGATCTGCAATCTTCGCCTCGGTATCTCTCTTGCTCCTCATCTGACTCCTG[T/G]
ACGTGTGGATGTCCTCCTTAAAACCAATCTTCCAAGGAATCACCCATTTCCCTCGTGTTCGTCCTGGATGCTCTGGAGTCTGCAGGGCGAGTGTCAGCTC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 41.30% | 3.80% | 45.96% | 9.01% | NA |
| All Indica | 2759 | 14.50% | 6.30% | 71.69% | 7.58% | NA |
| All Japonica | 1512 | 86.80% | 0.10% | 3.24% | 9.85% | NA |
| Aus | 269 | 71.00% | 0.00% | 27.88% | 1.12% | NA |
| Indica I | 595 | 27.90% | 1.50% | 65.71% | 4.87% | NA |
| Indica II | 465 | 8.20% | 4.70% | 67.31% | 19.78% | NA |
| Indica III | 913 | 7.80% | 10.30% | 78.53% | 3.40% | NA |
| Indica Intermediate | 786 | 15.80% | 6.10% | 70.87% | 7.25% | NA |
| Temperate Japonica | 767 | 95.60% | 0.10% | 1.69% | 2.61% | NA |
| Tropical Japonica | 504 | 78.20% | 0.00% | 6.15% | 15.67% | NA |
| Japonica Intermediate | 241 | 76.80% | 0.40% | 2.07% | 20.75% | NA |
| VI/Aromatic | 96 | 12.50% | 1.00% | 29.17% | 57.29% | NA |
| Intermediate | 90 | 40.00% | 2.20% | 46.67% | 11.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0808829838 | A -> C | LOC_Os08g14670.1 | missense_variant ; p.Tyr1407Ser; MODERATE | nonsynonymous_codon ; Y1407S | Average:9.131; most accessible tissue: Minghui63 panicle, score: 16.27 | benign  |
1.473 |
DELETERIOUS | 0.00 |
| vg0808829838 | A -> DEL | LOC_Os08g14670.1 | N | frameshift_variant | Average:9.131; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0808829838 | 3.10E-06 | NA | mr1198 | 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 |
| vg0808829838 | 6.60E-06 | 6.60E-06 | mr1198 | Ind_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 |
| vg0808829838 | NA | 6.42E-06 | mr1984 | 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 |
| vg0808829838 | NA | 4.86E-06 | mr1984 | Ind_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 |