Search for Variation information by Variation ID:
Detailed information for vg0905248850:
| Variant ID: vg0905248850 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 5248850 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.79, C: 0.21, others allele: 0.00, population size: 28. )
Flanking Sequence (100 bp) in Reference Genome:
CTCGTCCAAAGACTTTGATAGTTTATCGCATCTGATACAGAAGGTAATCTTGCATGAGCATAGGTCGGCAGAGGTCAGGAAAAGCTCCAAGAAAGTTAAT[A/C]
ATGTTTGTCCATACATGTATGGGTCGGATGACGAAGAAGATGATTCTGAGATAGCTGCAGCTGCGTGGGTGAGGAGCAAAAAGGTCATACCATGCCAATG
Reverse complement sequence
CATTGGCATGGTATGACCTTTTTGCTCCTCACCCACGCAGCTGCAGCTATCTCAGAATCATCTTCTTCGTCATCCGACCCATACATGTATGGACAAACAT[T/G]
ATTAACTTTCTTGGAGCTTTTCCTGACCTCTGCCGACCTATGCTCATGCAAGATTACCTTCTGTATCAGATGCGATAAACTATCAAAGTCTTTGGACGAG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.90% | 7.60% | 18.05% | 41.52% | NA |
| All Indica | 2759 | 8.30% | 6.80% | 27.58% | 57.38% | NA |
| All Japonica | 1512 | 80.70% | 0.10% | 2.18% | 17.00% | NA |
| Aus | 269 | 22.70% | 60.60% | 11.52% | 5.20% | NA |
| Indica I | 595 | 15.10% | 0.30% | 14.45% | 70.08% | NA |
| Indica II | 465 | 9.50% | 8.80% | 19.35% | 62.37% | NA |
| Indica III | 913 | 3.10% | 5.10% | 40.96% | 50.82% | NA |
| Indica Intermediate | 786 | 8.40% | 12.30% | 26.84% | 52.42% | NA |
| Temperate Japonica | 767 | 90.10% | 0.00% | 0.39% | 9.52% | NA |
| Tropical Japonica | 504 | 82.10% | 0.20% | 4.76% | 12.90% | NA |
| Japonica Intermediate | 241 | 47.70% | 0.40% | 2.49% | 49.38% | NA |
| VI/Aromatic | 96 | 2.10% | 5.20% | 13.54% | 79.17% | NA |
| Intermediate | 90 | 47.80% | 0.00% | 16.67% | 35.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0905248850 | A -> DEL | LOC_Os09g09700.1 | N | frameshift_variant | Average:8.86; most accessible tissue: Callus, score: 31.081 | N | N | N | N |
| vg0905248850 | A -> C | LOC_Os09g09700.1 | missense_variant ; p.Asn514His; MODERATE | nonsynonymous_codon | Average:8.86; most accessible tissue: Callus, score: 31.081 | possibly damaging  |
-1.689 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0905248850 | NA | 1.02E-07 | mr1904_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 |
| vg0905248850 | NA | 8.09E-06 | mr1982_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 |