Search for Variation information by Variation ID:
Detailed information for vg1012595235:
| Variant ID: vg1012595235 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12595235 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GAATTTGAAAGATTAAATTTGGGAATTGTCAGTAGAGGTTTTGTTGCAGCCTTAGAAGCGAAGCCCACACTAATTGATCAAGTTAGAGAAGCTCAAATTA[G/A]
TGATCCTGATATTCAAGAGATCAAGAAGAATATGAGAAGAGGAAAAGCTATCGGTTTCTTGGAGGATGAGCAAGGAACTGTATGGTTGGGCGAGAGAATT
Reverse complement sequence
AATTCTCTCGCCCAACCATACAGTTCCTTGCTCATCCTCCAAGAAACCGATAGCTTTTCCTCTTCTCATATTCTTCTTGATCTCTTGAATATCAGGATCA[C/T]
TAATTTGAGCTTCTCTAACTTGATCAATTAGTGTGGGCTTCGCTTCTAAGGCTGCAACAAAACCTCTACTGACAATTCCCAAATTTAATCTTTCAAATTC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 63.80% | 0.60% | 15.87% | 19.74% | NA |
| All Indica | 2759 | 46.20% | 0.90% | 25.52% | 27.36% | NA |
| All Japonica | 1512 | 90.90% | 0.00% | 1.92% | 7.14% | NA |
| Aus | 269 | 83.60% | 1.50% | 3.35% | 11.52% | NA |
| Indica I | 595 | 28.60% | 0.50% | 21.51% | 49.41% | NA |
| Indica II | 465 | 34.00% | 0.90% | 30.54% | 34.62% | NA |
| Indica III | 913 | 64.80% | 1.10% | 25.63% | 8.43% | NA |
| Indica Intermediate | 786 | 45.00% | 1.10% | 25.45% | 28.37% | NA |
| Temperate Japonica | 767 | 97.50% | 0.00% | 0.52% | 1.96% | NA |
| Tropical Japonica | 504 | 83.70% | 0.00% | 3.57% | 12.70% | NA |
| Japonica Intermediate | 241 | 85.10% | 0.00% | 2.90% | 12.03% | NA |
| VI/Aromatic | 96 | 67.70% | 0.00% | 3.12% | 29.17% | NA |
| Intermediate | 90 | 82.20% | 0.00% | 5.56% | 12.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012595235 | G -> A | LOC_Os10g24540.1 | missense_variant ; p.Ser916Asn; MODERATE | nonsynonymous_codon ; S916N | Average:8.986; most accessible tissue: Callus, score: 19.854 | possibly damaging  |
-1.576 |
TOLERATED | 1.00 |
| vg1012595235 | G -> DEL | LOC_Os10g24540.1 | N | frameshift_variant | Average:8.986; most accessible tissue: Callus, score: 19.854 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1012595235 | NA | 9.31E-07 | mr1756 | 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 |
| vg1012595235 | NA | 3.95E-07 | mr1668_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 |
| vg1012595235 | 1.86E-07 | NA | mr1668_2 | Jap_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 |