Search for Variation information by Variation ID:
Detailed information for vg0210606536:
| Variant ID: vg0210606536 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 10606536 |
| 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: 209. )
Flanking Sequence (100 bp) in Reference Genome:
GGATTGAGCATGAGGCGATATTGTCGGAGGTTGTCGAACGTTTCCCGCAGATCGTCAATCAATGAGTTGCTTGTCTTAGTCTTGACAACAATGTCGTCGA[C/T]
GTAGGCCTCGACATTATTTCCAAGCTGGTCGCTAAGTGCACCCTGTACCGTGCGCTGGAAAGTATTCCCTGCGGTTATTAGTCTGAACGGCATCTTAACG
Reverse complement sequence
CGTTAAGATGCCGTTCAGACTAATAACCGCAGGGAATACTTTCCAGCGCACGGTACAGGGTGCACTTAGCGACCAGCTTGGAAATAATGTCGAGGCCTAC[G/A]
TCGACGACATTGTTGTCAAGACTAAGACAAGCAACTCATTGATTGACGATCTGCGGGAAACGTTCGACAACCTCCGACAATATCGCCTCATGCTCAATCC
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 | 56.50% | 14.40% | 15.51% | 13.58% | NA |
| All Indica | 2759 | 41.10% | 14.70% | 22.73% | 21.53% | NA |
| All Japonica | 1512 | 82.70% | 15.80% | 1.12% | 0.40% | NA |
| Aus | 269 | 56.90% | 0.00% | 31.23% | 11.90% | NA |
| Indica I | 595 | 37.80% | 24.40% | 20.00% | 17.82% | NA |
| Indica II | 465 | 50.30% | 3.90% | 24.09% | 21.72% | NA |
| Indica III | 913 | 35.80% | 17.20% | 23.66% | 23.33% | NA |
| Indica Intermediate | 786 | 44.10% | 10.80% | 22.90% | 22.14% | NA |
| Temperate Japonica | 767 | 99.10% | 0.10% | 0.65% | 0.13% | NA |
| Tropical Japonica | 504 | 60.10% | 37.30% | 1.59% | 0.99% | NA |
| Japonica Intermediate | 241 | 77.60% | 20.70% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 76.00% | 22.90% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 68.90% | 15.60% | 4.44% | 11.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0210606536 | C -> T | LOC_Os02g18290.1 | missense_variant ; p.Val878Ile; MODERATE | nonsynonymous_codon ; V878I | Average:25.752; most accessible tissue: Zhenshan97 flag leaf, score: 67.785 | benign  |
0.641 |
DELETERIOUS | 0.05 |
| vg0210606536 | C -> DEL | LOC_Os02g18290.1 | N | frameshift_variant | Average:25.752; most accessible tissue: Zhenshan97 flag leaf, score: 67.785 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0210606536 | NA | 2.82E-08 | mr1696 | Jap_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 |
| vg0210606536 | 1.05E-06 | 1.05E-06 | mr1714 | Jap_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 |
| vg0210606536 | NA | 4.18E-06 | mr1377_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 |