Search for Variation information by Variation ID:
Detailed information for vg0312663464:
| Variant ID: vg0312663464 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 12663464 |
| 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: 218. )
Flanking Sequence (100 bp) in Reference Genome:
ATTTGATGGATTTTATAGCCATATGCAGCAGCCAGTGCTACAAGAGCACGAATTGTAGGCATGTGAGCCACTGGAGAAAATGTATCAAAGTAATCTTCTC[C/T]
CTGTCTTTGTGTGTACCCCTTTGCGACCAACCTGGCTTTGAACTTGTCAATAGTTCCATCAGGTTTCAGTTTCTTGCAGCCTATGGCCCTATAGCCTATG
Reverse complement sequence
CATAGGCTATAGGGCCATAGGCTGCAAGAAACTGAAACCTGATGGAACTATTGACAAGTTCAAAGCCAGGTTGGTCGCAAAGGGGTACACACAAAGACAG[G/A]
GAGAAGATTACTTTGATACATTTTCTCCAGTGGCTCACATGCCTACAATTCGTGCTCTTGTAGCACTGGCTGCTGCATATGGCTATAAAATCCATCAAAT
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% | 29.90% | 3.58% | 5.42% | NA |
| All Indica | 2759 | 35.00% | 49.70% | 6.05% | 9.28% | NA |
| All Japonica | 1512 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 47.90% | 49.40% | 2.35% | 0.34% | NA |
| Indica II | 465 | 15.50% | 62.80% | 9.46% | 12.26% | NA |
| Indica III | 913 | 35.20% | 41.50% | 7.34% | 15.99% | NA |
| Indica Intermediate | 786 | 36.50% | 51.70% | 5.34% | 6.49% | NA |
| Temperate Japonica | 767 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 70.00% | 27.80% | 2.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0312663464 | C -> T | LOC_Os03g22100.1 | missense_variant ; p.Gly757Arg; MODERATE | nonsynonymous_codon ; G757R | Average:26.698; most accessible tissue: Zhenshan97 panicle, score: 63.607 | probably damaging  |
3.02 |
DELETERIOUS | 0.00 |
| vg0312663464 | C -> DEL | LOC_Os03g22100.1 | N | frameshift_variant | Average:26.698; most accessible tissue: Zhenshan97 panicle, score: 63.607 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0312663464 | 4.63E-06 | NA | mr1329 | 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 |
| vg0312663464 | 9.93E-07 | 9.93E-07 | mr1329 | 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 |
| vg0312663464 | NA | 3.58E-07 | mr1542 | 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 |
| vg0312663464 | NA | 2.27E-06 | mr1728 | 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 |
| vg0312663464 | NA | 2.24E-08 | mr1542_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 |