Search for Variation information by Variation ID:
Detailed information for vg0617641436:
| Variant ID: vg0617641436 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 17641436 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 66. )
Flanking Sequence (100 bp) in Reference Genome:
CGTTTGGAAGGAGAATAAAAGTGGAGCTTCAACTTCTAAGGCCCCTAGGAAGACCAAAGTAACTTTTGATATGCTTTTGGAGAAGTATGAGAAGCAAGGT[A/G]
GTGAGAGAGGTCGCAACAAAGGGAAAAGACCAAGATCACCTCCTAGGGAGCAATTTGGTCATTCATCAAGACGGTCGTATTCACCTCCATATCATCATCC
Reverse complement sequence
GGATGATGATATGGAGGTGAATACGACCGTCTTGATGAATGACCAAATTGCTCCCTAGGAGGTGATCTTGGTCTTTTCCCTTTGTTGCGACCTCTCTCAC[T/C]
ACCTTGCTTCTCATACTTCTCCAAAAGCATATCAAAAGTTACTTTGGTCTTCCTAGGGGCCTTAGAAGTTGAAGCTCCACTTTTATTCTCCTTCCAAACG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.10% | 10.60% | 8.34% | 46.00% | NA |
| All Indica | 2759 | 8.80% | 10.30% | 9.71% | 71.22% | NA |
| All Japonica | 1512 | 88.30% | 8.90% | 0.33% | 2.51% | NA |
| Aus | 269 | 15.60% | 4.10% | 33.09% | 47.21% | NA |
| Indica I | 595 | 15.00% | 9.10% | 7.23% | 68.74% | NA |
| Indica II | 465 | 9.90% | 5.20% | 3.87% | 81.08% | NA |
| Indica III | 913 | 1.90% | 13.90% | 13.58% | 70.65% | NA |
| Indica Intermediate | 786 | 11.50% | 10.10% | 10.56% | 67.94% | NA |
| Temperate Japonica | 767 | 95.80% | 0.10% | 0.13% | 3.91% | NA |
| Tropical Japonica | 504 | 76.40% | 22.60% | 0.60% | 0.40% | NA |
| Japonica Intermediate | 241 | 89.20% | 7.90% | 0.41% | 2.49% | NA |
| VI/Aromatic | 96 | 3.10% | 60.40% | 23.96% | 12.50% | NA |
| Intermediate | 90 | 38.90% | 15.60% | 10.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0617641436 | A -> G | LOC_Os06g30510.1 | missense_variant ; p.Ser377Gly; MODERATE | nonsynonymous_codon ; S377G | Average:7.085; most accessible tissue: Callus, score: 26.958 | benign  |
-0.826 |
TOLERATED | 1.00 |
| vg0617641436 | A -> DEL | LOC_Os06g30510.1 | N | frameshift_variant | Average:7.085; most accessible tissue: Callus, score: 26.958 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0617641436 | 2.54E-06 | NA | mr1096 | 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 |
| vg0617641436 | 1.61E-06 | NA | mr1108 | 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 |
| vg0617641436 | 2.86E-07 | NA | mr1108 | 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 |
| vg0617641436 | 6.16E-06 | NA | mr1111 | 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 |
| vg0617641436 | 5.06E-06 | NA | mr1121 | 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 |
| vg0617641436 | 7.93E-06 | 5.46E-06 | mr1121 | Ind_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 |