Search for Variation information by Variation ID:
Detailed information for vg0820512018:
| Variant ID: vg0820512018 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 20512018 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.08, others allele: 0.00, population size: 112. )
Flanking Sequence (100 bp) in Reference Genome:
TCAGAGCTTGGTCTCTCTTGATTGGGCTTCACCGCCTAGAGAGAAGATGTCGGACGAGGTGAACCATGTAGAGAAGGCTCCCATGTTTAATGGCACAAAC[C/T]
ACTCCACTTGGAAAATTAAAATGTCTACTCACCTCAAAGCTGTGAGCTTCCATATTTGGAGTATTGTGGATGTAGGCTTTGCTATCACCAGCACGCCCTT
Reverse complement sequence
AAGGGCGTGCTGGTGATAGCAAAGCCTACATCCACAATACTCCAAATATGGAAGCTCACAGCTTTGAGGTGAGTAGACATTTTAATTTTCCAAGTGGAGT[G/A]
GTTTGTGCCATTAAACATGGGAGCCTTCTCTACATGGTTCACCTCGTCCGACATCTTCTCTCTAGGCGGTGAAGCCCAATCAAGAGAGACCAAGCTCTGA
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 | 41.20% | 1.80% | 53.00% | 4.02% | NA |
| All Indica | 2759 | 14.10% | 2.50% | 76.91% | 6.49% | NA |
| All Japonica | 1512 | 92.90% | 0.10% | 6.94% | 0.13% | NA |
| Aus | 269 | 1.10% | 4.80% | 90.71% | 3.35% | NA |
| Indica I | 595 | 4.00% | 1.00% | 83.70% | 11.26% | NA |
| Indica II | 465 | 16.60% | 1.90% | 72.47% | 9.03% | NA |
| Indica III | 913 | 17.60% | 1.90% | 79.74% | 0.77% | NA |
| Indica Intermediate | 786 | 16.20% | 4.70% | 71.12% | 8.02% | NA |
| Temperate Japonica | 767 | 92.60% | 0.00% | 7.43% | 0.00% | NA |
| Tropical Japonica | 504 | 92.30% | 0.00% | 7.54% | 0.20% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.40% | 4.15% | 0.41% | NA |
| VI/Aromatic | 96 | 93.80% | 0.00% | 6.25% | 0.00% | NA |
| Intermediate | 90 | 65.60% | 3.30% | 31.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0820512018 | C -> T | LOC_Os08g33040.1 | missense_variant ; p.His19Tyr; MODERATE | nonsynonymous_codon ; H19Y | Average:37.047; most accessible tissue: Minghui63 flag leaf, score: 59.244 | probably damaging  |
-2.025 |
TOLERATED | 1.00 |
| vg0820512018 | C -> DEL | LOC_Os08g33040.1 | N | frameshift_variant | Average:37.047; most accessible tissue: Minghui63 flag leaf, score: 59.244 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0820512018 | 4.55E-06 | 5.40E-37 | mr1719 | 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 |
| vg0820512018 | 3.02E-06 | NA | mr1719 | 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 |
| vg0820512018 | NA | 6.67E-16 | mr1587_2 | 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 |