Search for Variation information by Variation ID:
Detailed information for vg1010618338:
| Variant ID: vg1010618338 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 10618338 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 122. )
Flanking Sequence (100 bp) in Reference Genome:
AAGAAACCATCAAAGGGAACAAAGCGCAAGAAACCCGAAAAGAATATGAAACAAGGGGATAGTAAGAAGCAAGATGATAGTTCGAAGCCAGATGATAAAC[T/C]
CCCTCCCCCATTCAAGAAGCATTCCATATTTTTTAAGTACCTCCCATACTGGAAAGATCTGGAAGTTCGGCATGCCATAGACGTCATGCATCTAGAGAAG
Reverse complement sequence
CTTCTCTAGATGCATGACGTCTATGGCATGCCGAACTTCCAGATCTTTCCAGTATGGGAGGTACTTAAAAAATATGGAATGCTTCTTGAATGGGGGAGGG[A/G]
GTTTATCATCTGGCTTCGAACTATCATCTTGCTTCTTACTATCCCCTTGTTTCATATTCTTTTCGGGTTTCTTGCGCTTTGTTCCCTTTGATGGTTTCTT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.00% | 8.60% | 0.38% | 0.00% | NA |
| All Indica | 2759 | 84.90% | 14.50% | 0.62% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.20% | 1.70% | 0.17% | 0.00% | NA |
| Indica II | 465 | 90.10% | 9.50% | 0.43% | 0.00% | NA |
| Indica III | 913 | 74.50% | 24.50% | 0.99% | 0.00% | NA |
| Indica Intermediate | 786 | 83.80% | 15.50% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 5.60% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1010618338 | T -> C | LOC_Os10g20970.1 | missense_variant ; p.Leu487Pro; MODERATE | nonsynonymous_codon ; L487P | Average:18.417; most accessible tissue: Minghui63 panicle, score: 38.588 | probably damaging  |
2.439 |
TOLERATED | 0.18 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1010618338 | NA | 1.27E-06 | mr1080 | 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 |
| vg1010618338 | NA | 5.95E-06 | mr1140 | 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 |
| vg1010618338 | NA | 5.22E-06 | mr1395 | 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 |
| vg1010618338 | NA | 4.80E-08 | mr1619 | 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 |