Search for Variation information by Variation ID:
Detailed information for vg1007896788:
| Variant ID: vg1007896788 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7896788 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGACAAATTCATTATACTTTTGCTTAACCGATGTCAAATCACATAACCTAAGCTCAGTTTCTCCAGTATAGAAATAATCATGAAATTGTTCTTCTAATTG[A/C]
ACCCAAGTATGAATAGAATTTGCCGGTAAAGAAGTAAACCATGTGAAAGCATTACCGGATAAAGATAGAGAAAACAAGCGCAATTTAAAAGTATCACTAT
Reverse complement sequence
ATAGTGATACTTTTAAATTGCGCTTGTTTTCTCTATCTTTATCCGGTAATGCTTTCACATGGTTTACTTCTTTACCGGCAAATTCTATTCATACTTGGGT[T/G]
CAATTAGAAGAACAATTTCATGATTATTTCTATACTGGAGAAACTGAGCTTAGGTTATGTGATTTGACATCGGTTAAGCAAAAGTATAATGAATTTGTCA
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 | 68.00% | 9.00% | 21.67% | 1.31% | NA |
| All Indica | 2759 | 65.70% | 13.20% | 21.09% | 0.00% | NA |
| All Japonica | 1512 | 74.70% | 0.10% | 21.10% | 4.10% | NA |
| Aus | 269 | 41.30% | 21.20% | 37.55% | 0.00% | NA |
| Indica I | 595 | 69.40% | 8.20% | 22.35% | 0.00% | NA |
| Indica II | 465 | 82.20% | 6.50% | 11.40% | 0.00% | NA |
| Indica III | 913 | 49.80% | 24.90% | 25.30% | 0.00% | NA |
| Indica Intermediate | 786 | 71.80% | 7.30% | 20.99% | 0.00% | NA |
| Temperate Japonica | 767 | 84.70% | 0.00% | 12.78% | 2.48% | NA |
| Tropical Japonica | 504 | 60.90% | 0.20% | 33.73% | 5.16% | NA |
| Japonica Intermediate | 241 | 71.80% | 0.00% | 21.16% | 7.05% | NA |
| VI/Aromatic | 96 | 85.40% | 2.10% | 12.50% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 4.40% | 11.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1007896788 | A -> C | LOC_Os10g15079.1 | synonymous_variant ; p.Val580Val; LOW | synonymous_codon | Average:16.014; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
| vg1007896788 | A -> C | LOC_Os10g15079.1 | synonymous_variant ; p.Val580Val; LOW | nonsynonymous_codon ; V580A | Average:16.014; most accessible tissue: Minghui63 panicle, score: 25.313 | possibly damaging  |
-1.548 |
TOLERATED | 1.00 |
| vg1007896788 | A -> DEL | LOC_Os10g15079.1 | N | frameshift_variant | Average:16.014; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1007896788 | 6.65E-07 | 7.12E-07 | mr1622_2 | 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 |