Search for Variation information by Variation ID:
Detailed information for vg0807538911:
| Variant ID: vg0807538911 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 7538911 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCTTCGGTAGTATCCTGCCAAACCCAAAAATCTGCGGACTTGAGTGACTGTCTTGGGTTGCTTCCAGTCAGTGACGGCGGTCACTATTTCAGGGTCCACA[G/A]
CAACTCCTTTAGCGGATATCACGTGCCCTAAGAATTTGACTTCGGACAACCAGAACTCACACTTGCTAAGCTTGGCATACAATTGATGTTCCCGCAACTT
Reverse complement sequence
AAGTTGCGGGAACATCAATTGTATGCCAAGCTTAGCAAGTGTGAGTTCTGGTTGTCCGAAGTCAAATTCTTAGGGCACGTGATATCCGCTAAAGGAGTTG[C/T]
TGTGGACCCTGAAATAGTGACCGCCGTCACTGACTGGAAGCAACCCAAGACAGTCACTCAAGTCCGCAGATTTTTGGGTTTGGCAGGATACTACCGAAGA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 55.50% | 1.10% | 10.88% | 32.52% | NA |
| All Indica | 2759 | 30.20% | 0.00% | 16.31% | 53.46% | NA |
| All Japonica | 1512 | 94.60% | 3.40% | 0.66% | 1.32% | NA |
| Aus | 269 | 81.80% | 0.00% | 13.01% | 5.20% | NA |
| Indica I | 595 | 17.10% | 0.00% | 6.39% | 76.47% | NA |
| Indica II | 465 | 52.30% | 0.00% | 7.96% | 39.78% | NA |
| Indica III | 913 | 23.90% | 0.00% | 27.38% | 48.74% | NA |
| Indica Intermediate | 786 | 34.50% | 0.00% | 15.90% | 49.62% | NA |
| Temperate Japonica | 767 | 91.90% | 5.10% | 1.17% | 1.83% | NA |
| Tropical Japonica | 504 | 98.80% | 0.40% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 94.60% | 4.10% | 0.41% | 0.83% | NA |
| VI/Aromatic | 96 | 82.30% | 0.00% | 14.58% | 3.12% | NA |
| Intermediate | 90 | 66.70% | 0.00% | 5.56% | 27.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0807538911 | G -> A | LOC_Os08g12720.1 | missense_variant ; p.Ala68Val; MODERATE | nonsynonymous_codon ; A68V | Average:24.125; most accessible tissue: Minghui63 panicle, score: 38.588 | benign  |
1.029 |
DELETERIOUS | 0.01 |
| vg0807538911 | G -> DEL | LOC_Os08g12720.1 | N | frameshift_variant | Average:24.125; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0807538911 | 9.92E-09 | 3.70E-08 | mr1038_2 | 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 |
| vg0807538911 | 7.45E-09 | 7.45E-09 | mr1191_2 | 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 |
| vg0807538911 | 7.89E-08 | 7.89E-08 | mr1389_2 | Jap_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 |