Search for Variation information by Variation ID:
Detailed information for vg1204092989:
| Variant ID: vg1204092989 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 4092989 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.02, others allele: 0.00, population size: 120. )
Flanking Sequence (100 bp) in Reference Genome:
TTGTGAATTTACTATTTACATTTACACACCGTGCAAGATCTCCTCGAGGCTGCCTCTCGCCATGTAGTCGTAGACCAGCATGAGCTTGGCGCTGCCGCCG[T/C]
CGTCGTCGAGGCAGAACCCGGCGAGCGGCATGGTGTTGTCGTGGCGGACGGAGCTGACGATCCCCATCTCCTAGACGAGCTCCTCCATCACCTTGTCTGA
Reverse complement sequence
TCAGACAAGGTGATGGAGGAGCTCGTCTAGGAGATGGGGATCGTCAGCTCCGTCCGCCACGACAACACCATGCCGCTCGCCGGGTTCTGCCTCGACGACG[A/G]
CGGCGGCAGCGCCAAGCTCATGCTGGTCTACGACTACATGGCGAGAGGCAGCCTCGAGGAGATCTTGCACGGTGTGTAAATGTAAATAGTAAATTCACAA
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 | 42.20% | 33.70% | 17.94% | 6.09% | NA |
| All Indica | 2759 | 31.50% | 34.90% | 25.77% | 7.83% | NA |
| All Japonica | 1512 | 57.60% | 33.20% | 5.42% | 3.77% | NA |
| Aus | 269 | 43.10% | 37.20% | 15.61% | 4.09% | NA |
| Indica I | 595 | 13.30% | 39.80% | 41.68% | 5.21% | NA |
| Indica II | 465 | 21.50% | 32.30% | 34.41% | 11.83% | NA |
| Indica III | 913 | 46.90% | 33.60% | 12.38% | 7.12% | NA |
| Indica Intermediate | 786 | 33.20% | 34.40% | 24.17% | 8.27% | NA |
| Temperate Japonica | 767 | 81.50% | 14.60% | 2.09% | 1.83% | NA |
| Tropical Japonica | 504 | 37.90% | 54.20% | 5.36% | 2.58% | NA |
| Japonica Intermediate | 241 | 22.80% | 48.50% | 16.18% | 12.45% | NA |
| VI/Aromatic | 96 | 90.60% | 4.20% | 5.21% | 0.00% | NA |
| Intermediate | 90 | 60.00% | 26.70% | 8.89% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1204092989 | T -> C | LOC_Os12g08050.1 | missense_variant ; p.Asp23Gly; MODERATE | nonsynonymous_codon ; D23G | Average:39.19; most accessible tissue: Callus, score: 84.474 | benign  |
-0.232 |
TOLERATED | 0.09 |
| vg1204092989 | T -> DEL | LOC_Os12g08050.1 | N | frameshift_variant | Average:39.19; most accessible tissue: Callus, score: 84.474 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1204092989 | 4.50E-06 | 4.14E-06 | mr1800 | 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 |