Search for Variation information by Variation ID:
Detailed information for vg0906569622:
| Variant ID: vg0906569622 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 6569622 |
| 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, T: 0.00, others allele: 0.00, population size: 336. )
Flanking Sequence (100 bp) in Reference Genome:
TTTAAAGACTTTGGAAAGGATGCACGAAACATACGGTTTGGTTTAAGTACGGATGGCATGAATCCTTTTGGAGAGATGAGCAGTGGCCATAGCACTTGGC[C/T]
CGTTACGATGTGTATCTACAACCTCCCCCCGTGGTTATGCATGAAGAGGAAGTACATAATGATACCGATTATAATTCAAGGCCCCAAGCAACCTGTTAAC
Reverse complement sequence
GTTAACAGGTTGCTTGGGGCCTTGAATTATAATCGGTATCATTATGTACTTCCTCTTCATGCATAACCACGGGGGGAGGTTGTAGATACACATCGTAACG[G/A]
GCCAAGTGCTATGGCCACTGCTCATCTCTCCAAAAGGATTCATGCCATCCGTACTTAAACCAAACCGTATGTTTCGTGCATCCTTTCCAAAGTCTTTAAA
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 | 72.30% | 27.10% | 0.61% | 0.00% | NA |
| All Indica | 2759 | 53.30% | 45.70% | 1.01% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 31.10% | 65.40% | 3.53% | 0.00% | NA |
| Indica II | 465 | 69.20% | 30.30% | 0.43% | 0.00% | NA |
| Indica III | 913 | 53.90% | 45.70% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 59.90% | 39.90% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 17.80% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0906569622 | C -> T | LOC_Os09g11750.1 | missense_variant ; p.Pro190Leu; MODERATE | nonsynonymous_codon ; P190L | Average:42.327; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 | benign  |
1.073 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0906569622 | NA | 5.28E-08 | mr1308 | 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 |