Search for Variation information by Variation ID:
Detailed information for vg0518963862:
| Variant ID: vg0518963862 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 18963862 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.57, G: 0.43, others allele: 0.00, population size: 97. )
Flanking Sequence (100 bp) in Reference Genome:
TGTTTTCGATGGAACGGATTTTTCTCATTGGTGTAGTAGGATGCAATCTTACATTATGGCTGAGAATTATGATATTTGGAGAAAAGTTTCTCATCCTTAT[A/G]
TGATTCCTGAAGTTATTAATACTGCTGCTGCAAAAACTGAGTTTGAACAAAATTGCAAAGCTCGCAATATTCTTTTGAGTGGGATTTCTCGTTCGGATTA
Reverse complement sequence
TAATCCGAACGAGAAATCCCACTCAAAAGAATATTGCGAGCTTTGCAATTTTGTTCAAACTCAGTTTTTGCAGCAGCAGTATTAATAACTTCAGGAATCA[T/C]
ATAAGGATGAGAAACTTTTCTCCAAATATCATAATTCTCAGCCATAATGTAAGATTGCATCCTACTACACCAATGAGAAAAATCCGTTCCATCGAAAACA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 27.90% | 16.20% | 1.08% | 54.80% | NA |
| All Indica | 2759 | 1.70% | 7.40% | 1.63% | 89.24% | NA |
| All Japonica | 1512 | 75.80% | 20.40% | 0.26% | 3.51% | NA |
| Aus | 269 | 1.10% | 83.60% | 0.37% | 14.87% | NA |
| Indica I | 595 | 0.70% | 0.50% | 1.18% | 97.65% | NA |
| Indica II | 465 | 2.60% | 28.80% | 0.65% | 67.96% | NA |
| Indica III | 913 | 1.40% | 1.40% | 2.08% | 95.07% | NA |
| Indica Intermediate | 786 | 2.40% | 6.90% | 2.04% | 88.68% | NA |
| Temperate Japonica | 767 | 87.70% | 8.60% | 0.13% | 3.52% | NA |
| Tropical Japonica | 504 | 63.50% | 31.70% | 0.20% | 4.56% | NA |
| Japonica Intermediate | 241 | 63.50% | 34.40% | 0.83% | 1.24% | NA |
| VI/Aromatic | 96 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 35.60% | 24.40% | 1.11% | 38.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0518963862 | A -> DEL | LOC_Os05g32470.1 | N | frameshift_variant | Average:10.288; most accessible tissue: Minghui63 root, score: 17.665 | N | N | N | N |
| vg0518963862 | A -> G | LOC_Os05g32470.1 | missense_variant ; p.Met44Val; MODERATE | nonsynonymous_codon ; M44V | Average:10.288; most accessible tissue: Minghui63 root, score: 17.665 | benign  |
-1.234 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0518963862 | 1.99E-06 | NA | mr1301 | 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 |
| vg0518963862 | 6.70E-07 | NA | mr1301_2 | 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 |
| vg0518963862 | NA | 9.03E-06 | mr1322_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 |
| vg0518963862 | 3.67E-06 | NA | mr1410_2 | 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 |