Search for Variation information by Variation ID:
Detailed information for vg0911104766:
| Variant ID: vg0911104766 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 11104766 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, A: 0.07, others allele: 0.00, population size: 86. )
Flanking Sequence (100 bp) in Reference Genome:
AAACTTCCATGGAACATTGGAGCCAATGCCCCTTGTTCGTCCACGGTGTTCTTCGTTTCCCAATGCTTTCGTGAGGATGTCATCCTCGCGTTTTTGTGAG[C/A]
AAACCTCTTGGGAGGCCTGTCTCTCAGCATTCAGTTCGACCTAGAGTACAGTTAGGATGCGTTAGACGAACAACAAGATACAACATAATGAAACTTATTC
Reverse complement sequence
GAATAAGTTTCATTATGTTGTATCTTGTTGTTCGTCTAACGCATCCTAACTGTACTCTAGGTCGAACTGAATGCTGAGAGACAGGCCTCCCAAGAGGTTT[G/T]
CTCACAAAAACGCGAGGATGACATCCTCACGAAAGCATTGGGAAACGAAGAACACCGTGGACGAACAAGGGGCATTGGCTCCAATGTTCCATGGAAGTTT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 49.60% | 34.70% | 5.14% | 10.50% | NA |
| All Indica | 2759 | 33.30% | 56.70% | 5.07% | 4.89% | NA |
| All Japonica | 1512 | 86.60% | 1.40% | 1.52% | 10.45% | NA |
| Aus | 269 | 13.80% | 15.20% | 22.68% | 48.33% | NA |
| Indica I | 595 | 19.50% | 72.90% | 3.03% | 4.54% | NA |
| Indica II | 465 | 41.10% | 35.90% | 11.40% | 11.61% | NA |
| Indica III | 913 | 39.10% | 57.10% | 2.63% | 1.20% | NA |
| Indica Intermediate | 786 | 32.60% | 56.20% | 5.73% | 5.47% | NA |
| Temperate Japonica | 767 | 87.90% | 0.70% | 1.17% | 10.30% | NA |
| Tropical Japonica | 504 | 93.50% | 1.60% | 1.19% | 3.77% | NA |
| Japonica Intermediate | 241 | 68.50% | 3.30% | 3.32% | 24.90% | NA |
| VI/Aromatic | 96 | 21.90% | 4.20% | 13.54% | 60.42% | NA |
| Intermediate | 90 | 63.30% | 13.30% | 6.67% | 16.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0911104766 | C -> DEL | LOC_Os09g18120.1 | N | frameshift_variant | Average:33.391; most accessible tissue: Minghui63 young leaf, score: 48.378 | N | N | N | N |
| vg0911104766 | C -> A | LOC_Os09g18120.1 | missense_variant ; p.Cys451Phe; MODERATE | nonsynonymous_codon ; C451F | Average:33.391; most accessible tissue: Minghui63 young leaf, score: 48.378 | probably damaging  |
2.013 |
TOLERATED | 0.66 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0911104766 | 1.89E-06 | 1.89E-06 | mr1623 | 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 |