Search for Variation information by Variation ID:
Detailed information for vg0230036264:
| Variant ID: vg0230036264 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 30036264 |
| 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: 268. )
Flanking Sequence (100 bp) in Reference Genome:
AACTCCTCTTGCATCGCCATCACCCAATCTAGATCATTTAAGAGCTTCTTCCACCCTTAGAGGTTCAAGAGAAGACACAAACGAGTAATGCTCACAAAAA[T/C]
TTGCGATACGAGAACGAGTGGATACTCCCTTGTTGATGTCTCCTAAGATGTTGTCGGTGAGATGATCTCTTTGGATGCTTTGGTGGATTCTTGGGCGAGC
Reverse complement sequence
GCTCGCCCAAGAATCCACCAAAGCATCCAAAGAGATCATCTCACCGACAACATCTTAGGAGACATCAACAAGGGAGTATCCACTCGTTCTCGTATCGCAA[A/G]
TTTTTGTGAGCATTACTCGTTTGTGTCTTCTCTTGAACCTCTAAGGGTGGAAGAAGCTCTTAAATGATCTAGATTGGGTGATGGCGATGCAAGAGGAGTT
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 | 91.80% | 7.50% | 0.70% | 0.00% | NA |
| All Indica | 2759 | 86.20% | 12.60% | 1.16% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.00% | 0.50% | 0.00% | NA |
| Indica II | 465 | 54.80% | 41.50% | 3.66% | 0.00% | NA |
| Indica III | 913 | 94.10% | 5.60% | 0.33% | 0.00% | NA |
| Indica Intermediate | 786 | 85.50% | 13.40% | 1.15% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 4.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0230036264 | T -> C | LOC_Os02g49120.1 | missense_variant ; p.Asn1018Ser; MODERATE | nonsynonymous_codon | Average:23.161; most accessible tissue: Minghui63 root, score: 33.152 | benign  |
1.207 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0230036264 | NA | 3.38E-06 | mr1336_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 |
| vg0230036264 | NA | 4.98E-08 | mr1712_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 |
| vg0230036264 | NA | 1.33E-06 | mr1732_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 |
| vg0230036264 | NA | 1.06E-06 | mr1946_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 |
| vg0230036264 | NA | 1.06E-06 | mr1948_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 |
| vg0230036264 | NA | 8.91E-06 | mr1977_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 |