Search for Variation information by Variation ID:
Detailed information for vg0806818905:
| Variant ID: vg0806818905 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 6818905 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 304. )
Flanking Sequence (100 bp) in Reference Genome:
TACGGAAGGACGACAGTTACCATTGGAATTATGCAAGGAATTTGAAAGATTAAATTTGGGAATTGTCAGTAGAGGTTTCGTTGCAGCCTTAGAAGCGAAG[T/C]
CCACTCTAATTGATCAAGTTAGAGAAGCCCAAATTAATGATCCTGATATTCAAGAAATCAAGAAGAATATGAGAAGAGGAAAAGCTATCGGTTTCTTGGA
Reverse complement sequence
TCCAAGAAACCGATAGCTTTTCCTCTTCTCATATTCTTCTTGATTTCTTGAATATCAGGATCATTAATTTGGGCTTCTCTAACTTGATCAATTAGAGTGG[A/G]
CTTCGCTTCTAAGGCTGCAACGAAACCTCTACTGACAATTCCCAAATTTAATCTTTCAAATTCCTTGCATAATTCCAATGGTAACTGTCGTCCTTCCGTA
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 | 58.10% | 31.30% | 7.22% | 3.41% | NA |
| All Indica | 2759 | 79.60% | 8.90% | 11.45% | 0.00% | NA |
| All Japonica | 1512 | 9.90% | 78.40% | 1.12% | 10.58% | NA |
| Aus | 269 | 98.10% | 1.50% | 0.37% | 0.00% | NA |
| Indica I | 595 | 81.80% | 13.60% | 4.54% | 0.00% | NA |
| Indica II | 465 | 83.70% | 8.80% | 7.53% | 0.00% | NA |
| Indica III | 913 | 75.50% | 6.40% | 18.18% | 0.00% | NA |
| Indica Intermediate | 786 | 80.40% | 8.40% | 11.20% | 0.00% | NA |
| Temperate Japonica | 767 | 14.00% | 65.40% | 1.04% | 19.56% | NA |
| Tropical Japonica | 504 | 3.80% | 94.40% | 1.39% | 0.40% | NA |
| Japonica Intermediate | 241 | 10.00% | 85.90% | 0.83% | 3.32% | NA |
| VI/Aromatic | 96 | 92.70% | 4.20% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 50.00% | 44.40% | 4.44% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0806818905 | T -> C | LOC_Os08g11620.1 | missense_variant ; p.Ser527Pro; MODERATE | nonsynonymous_codon ; S527P | Average:12.788; most accessible tissue: Zhenshan97 flag leaf, score: 17.677 | benign  |
-0.275 |
TOLERATED | 1.00 |
| vg0806818905 | T -> DEL | LOC_Os08g11620.1 | N | frameshift_variant | Average:12.788; most accessible tissue: Zhenshan97 flag leaf, score: 17.677 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0806818905 | NA | 6.82E-06 | mr1415 | 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 |
| vg0806818905 | NA | 6.82E-06 | mr1567 | 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 |
| vg0806818905 | NA | 8.84E-08 | mr1062_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 |
| vg0806818905 | 4.00E-09 | 3.36E-08 | mr1588_2 | 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 |