Search for Variation information by Variation ID:
Detailed information for vg1006588076:
| Variant ID: vg1006588076 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 6588076 |
| 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, others allele: 0.00, population size: 291. )
Flanking Sequence (100 bp) in Reference Genome:
AACAATTTCTTCTCTTCAGAATTCATTGAGTATGGGGCTGGAGGTAAATAAAATTTATCTTCTACTTCAATAGGATGAAGATCACTTCTTATGCCTAGAG[C/T]
TTGAAGGTCTAACCAAGAATTTAAGTTGTCTTTTGACTTCTTGTCAGTACCCAAGAGTGTATTGATTATGTTATCACATACATTTTTCTCAATGTGCATT
Reverse complement sequence
AATGCACATTGAGAAAAATGTATGTGATAACATAATCAATACACTCTTGGGTACTGACAAGAAGTCAAAAGACAACTTAAATTCTTGGTTAGACCTTCAA[G/A]
CTCTAGGCATAAGAAGTGATCTTCATCCTATTGAAGTAGAAGATAAATTTTATTTACCTCCAGCCCCATACTCAATGAATTCTGAAGAGAAGAAATTGTT
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 | 79.00% | 1.50% | 0.36% | 19.17% | NA |
| All Indica | 2759 | 75.60% | 0.00% | 0.33% | 24.07% | NA |
| All Japonica | 1512 | 80.20% | 4.60% | 0.40% | 14.88% | NA |
| Aus | 269 | 97.00% | 0.00% | 0.00% | 2.97% | NA |
| Indica I | 595 | 84.00% | 0.00% | 0.17% | 15.80% | NA |
| Indica II | 465 | 84.10% | 0.00% | 0.22% | 15.70% | NA |
| Indica III | 913 | 66.60% | 0.00% | 0.55% | 32.86% | NA |
| Indica Intermediate | 786 | 74.70% | 0.00% | 0.25% | 25.06% | NA |
| Temperate Japonica | 767 | 76.40% | 8.10% | 0.52% | 14.99% | NA |
| Tropical Japonica | 504 | 87.10% | 0.20% | 0.40% | 12.30% | NA |
| Japonica Intermediate | 241 | 77.60% | 2.50% | 0.00% | 19.92% | NA |
| VI/Aromatic | 96 | 95.80% | 1.00% | 2.08% | 1.04% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 0.00% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1006588076 | C -> T | LOC_Os10g11870.1 | missense_variant ; p.Ala587Thr; MODERATE | nonsynonymous_codon ; A587T | Average:11.62; most accessible tissue: Callus, score: 18.723 | benign  |
1.253 |
TOLERATED | 0.43 |
| vg1006588076 | C -> DEL | LOC_Os10g11870.1 | N | frameshift_variant | Average:11.62; most accessible tissue: Callus, score: 18.723 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1006588076 | 3.12E-06 | NA | mr1024 | 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 |