Search for Variation information by Variation ID:
Detailed information for vg1006617495:
| Variant ID: vg1006617495 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 6617495 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, A: 0.12, others allele: 0.00, population size: 84. )
Flanking Sequence (100 bp) in Reference Genome:
CAAATCATGTTCAGTTTTCCTGGCAAGTTCCCTAGCTTCGTGCAGCTGGTTTCTGGTGGCCTCAAGGGTTCCAAGGTGGGGAACTAACCTCTCAAGAGTC[G/A]
CAGTTTTTGCTTCATTCCTGAGATGGATTCTCTGCAAAACAATTTTATTGGCATTTGAGCTAAGTGGCAAATAGGATGGTTGAGGCCGTGCATGAGGAAA
Reverse complement sequence
TTTCCTCATGCACGGCCTCAACCATCCTATTTGCCACTTAGCTCAAATGCCAATAAAATTGTTTTGCAGAGAATCCATCTCAGGAATGAAGCAAAAACTG[C/T]
GACTCTTGAGAGGTTAGTTCCCCACCTTGGAACCCTTGAGGCCACCAGAAACCAGCTGCACGAAGCTAGGGAACTTGCCAGGAAAACTGAACATGATTTG
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 | 47.10% | 23.30% | 14.68% | 15.00% | NA |
| All Indica | 2759 | 38.70% | 36.20% | 18.34% | 6.74% | NA |
| All Japonica | 1512 | 56.70% | 5.20% | 5.09% | 33.00% | NA |
| Aus | 269 | 68.40% | 0.70% | 30.48% | 0.37% | NA |
| Indica I | 595 | 46.90% | 10.10% | 34.79% | 8.24% | NA |
| Indica II | 465 | 26.50% | 60.00% | 8.82% | 4.73% | NA |
| Indica III | 913 | 41.60% | 36.40% | 15.12% | 6.90% | NA |
| Indica Intermediate | 786 | 36.50% | 41.60% | 15.27% | 6.62% | NA |
| Temperate Japonica | 767 | 81.20% | 8.70% | 2.61% | 7.43% | NA |
| Tropical Japonica | 504 | 17.50% | 0.60% | 5.75% | 76.19% | NA |
| Japonica Intermediate | 241 | 61.00% | 3.30% | 11.62% | 24.07% | NA |
| VI/Aromatic | 96 | 72.90% | 3.10% | 10.42% | 13.54% | NA |
| Intermediate | 90 | 47.80% | 20.00% | 21.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1006617495 | G -> A | LOC_Os10g11930.1 | missense_variant ; p.Ala422Val; MODERATE | nonsynonymous_codon ; A422V | Average:17.825; most accessible tissue: Callus, score: 36.571 | benign  |
0.094 |
TOLERATED | 0.09 |
| vg1006617495 | G -> DEL | LOC_Os10g11930.1 | N | frameshift_variant | Average:17.825; most accessible tissue: Callus, score: 36.571 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1006617495 | NA | 1.18E-13 | mr1709 | 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 |
| vg1006617495 | NA | 8.07E-12 | mr1709 | 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 |
| vg1006617495 | 1.39E-08 | 9.09E-11 | mr1027_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 |
| vg1006617495 | NA | 4.34E-07 | mr1580_2 | 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 |
| vg1006617495 | NA | 1.68E-11 | mr1709_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 |
| vg1006617495 | NA | 2.21E-11 | mr1709_2 | 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 |
| vg1006617495 | NA | 2.66E-07 | mr1825_2 | 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 |