Search for Variation information by Variation ID:
Detailed information for vg0327185700:
| Variant ID: vg0327185700 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 27185700 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, C: 0.06, others allele: 0.00, population size: 136. )
Flanking Sequence (100 bp) in Reference Genome:
AAAGCTTTTGACAATCTTAAAGAAGTTATGACTTCCTGTCCAGTTTTGGCTTTACCCAATTTCAATCAACCTTTTGTCCTAGAGACAGATGCATGTGGTA[T/C]
TGGAATTGGGGCTGTACTGATGCAAGAAGGGAGACCCATTGCTTATTTCAGCAAATCTCTGGGGAAGAAGGCAGCTAGCTCTTCAACATATGAAAAGGAG
Reverse complement sequence
CTCCTTTTCATATGTTGAAGAGCTAGCTGCCTTCTTCCCCAGAGATTTGCTGAAATAAGCAATGGGTCTCCCTTCTTGCATCAGTACAGCCCCAATTCCA[A/G]
TACCACATGCATCTGTCTCTAGGACAAAAGGTTGATTGAAATTGGGTAAAGCCAAAACTGGACAGGAAGTCATAACTTCTTTAAGATTGTCAAAAGCTTT
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 | 47.90% | 1.30% | 17.50% | 33.33% | NA |
| All Indica | 2759 | 24.00% | 2.20% | 27.94% | 45.81% | NA |
| All Japonica | 1512 | 98.90% | 0.00% | 0.00% | 1.12% | NA |
| Aus | 269 | 4.10% | 0.40% | 17.10% | 78.44% | NA |
| Indica I | 595 | 8.90% | 4.00% | 48.57% | 38.49% | NA |
| Indica II | 465 | 12.00% | 2.80% | 44.09% | 41.08% | NA |
| Indica III | 913 | 41.40% | 0.40% | 6.46% | 51.70% | NA |
| Indica Intermediate | 786 | 22.40% | 2.50% | 27.74% | 47.33% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 98.40% | 0.00% | 0.00% | 1.59% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 45.80% | 0.00% | 0.00% | 54.17% | NA |
| Intermediate | 90 | 54.40% | 0.00% | 11.11% | 34.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0327185700 | T -> C | LOC_Os03g47840.1 | missense_variant ; p.Ile679Thr; MODERATE | nonsynonymous_codon ; I679T | Average:14.049; most accessible tissue: Callus, score: 31.072 | benign  |
-1.341 |
TOLERATED | 0.60 |
| vg0327185700 | T -> DEL | LOC_Os03g47840.1 | N | frameshift_variant | Average:14.049; most accessible tissue: Callus, score: 31.072 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0327185700 | NA | 3.03E-13 | mr1874 | 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 |
| vg0327185700 | 2.95E-07 | NA | mr1928 | 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 |
| vg0327185700 | 3.28E-08 | 1.19E-06 | mr1928 | 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 |