Search for Variation information by Variation ID:
Detailed information for vg1013579576:
| Variant ID: vg1013579576 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 13579576 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 245. )
Flanking Sequence (100 bp) in Reference Genome:
AATAAAGCTACACCAAAGGACGAATATCCAATGCCAGTGGCCGATCAGCTGGTTGATGCCGCATCAGGGAACAAAATTTTGAGTTTTGTGGATGGGAACG[C/T]
AGGATATAATCAGATCTTTATGGCTGAGGAAGATATCCATAAGATGGCTTTTAGATGCCCTAGTGCAATCGGCTTATTTGAATGGGTCGTCATGACTTTT
Reverse complement sequence
AAAAGTCATGACGACCCATTCAAATAAGCCGATTGCACTAGGGCATCTAAAAGCCATCTTATGGATATCTTCCTCAGCCATAAAGATCTGATTATATCCT[G/A]
CGTTCCCATCCACAAAACTCAAAATTTTGTTCCCTGATGCGGCATCAACCAGCTGATCGGCCACTGGCATTGGATATTCGTCCTTTGGTGTAGCTTTATT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 61.20% | 20.10% | 18.58% | 0.06% | NA |
| All Indica | 2759 | 40.30% | 32.80% | 26.82% | 0.11% | NA |
| All Japonica | 1512 | 99.50% | 0.10% | 0.46% | 0.00% | NA |
| Aus | 269 | 47.20% | 11.50% | 41.26% | 0.00% | NA |
| Indica I | 595 | 46.90% | 18.80% | 34.12% | 0.17% | NA |
| Indica II | 465 | 20.20% | 44.10% | 35.48% | 0.22% | NA |
| Indica III | 913 | 45.10% | 36.90% | 17.96% | 0.00% | NA |
| Indica Intermediate | 786 | 41.50% | 31.90% | 26.46% | 0.13% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.20% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 87.50% | 3.10% | 9.38% | 0.00% | NA |
| Intermediate | 90 | 74.40% | 13.30% | 12.22% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1013579576 | C -> T | LOC_Os10g26210.1 | missense_variant ; p.Ala761Val; MODERATE | nonsynonymous_codon ; A761V | Average:20.092; most accessible tissue: Minghui63 flag leaf, score: 28.142 | benign  |
0.87 |
TOLERATED | 0.07 |
| vg1013579576 | C -> DEL | LOC_Os10g26210.1 | N | frameshift_variant | Average:20.092; most accessible tissue: Minghui63 flag leaf, score: 28.142 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1013579576 | NA | 3.82E-09 | mr1533 | 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 |
| vg1013579576 | 1.48E-06 | NA | mr1980 | 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 |
| vg1013579576 | 6.88E-07 | 2.72E-13 | mr1980 | 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 |
| vg1013579576 | 6.73E-06 | 1.25E-11 | mr1533_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 |
| vg1013579576 | NA | 1.47E-06 | mr1980_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 |