Search for Variation information by Variation ID:
Detailed information for vg0620350630:
| Variant ID: vg0620350630 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20350630 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, G: 0.03, others allele: 0.00, population size: 101. )
Flanking Sequence (100 bp) in Reference Genome:
TAGGTAGCCTCAAAATAACACTGGGAGAGAATGAATCTCAATTCCATTCTCGCGGGCAAGGATCACCTTGACCGACCCTCTCCTAGAAATTGAGTCAGCG[A/G]
AAGAGGTTACCGCAGTTCCTCCTCATGAGTCTCCCGAGGCCCTTCTGGAAGATGAGGTCCCCGACTTCATCAAGGAAGAAGCAGATCCCGGTGAGACTCT
Reverse complement sequence
AGAGTCTCACCGGGATCTGCTTCTTCCTTGATGAAGTCGGGGACCTCATCTTCCAGAAGGGCCTCGGGAGACTCATGAGGAGGAACTGCGGTAACCTCTT[T/C]
CGCTGACTCAATTTCTAGGAGAGGGTCGGTCAAGGTGATCCTTGCCCGCGAGAATGGAATTGAGATTCATTCTCTCCCAGTGTTATTTTGAGGCTACCTA
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 | 38.40% | 36.60% | 19.30% | 5.71% | NA |
| All Indica | 2759 | 61.90% | 8.50% | 28.63% | 1.01% | NA |
| All Japonica | 1512 | 1.30% | 92.90% | 4.70% | 1.06% | NA |
| Aus | 269 | 10.00% | 4.10% | 10.41% | 75.46% | NA |
| Indica I | 595 | 55.80% | 14.30% | 29.41% | 0.50% | NA |
| Indica II | 465 | 61.10% | 7.50% | 29.89% | 1.51% | NA |
| Indica III | 913 | 69.40% | 3.00% | 27.16% | 0.44% | NA |
| Indica Intermediate | 786 | 58.10% | 11.10% | 29.01% | 1.78% | NA |
| Temperate Japonica | 767 | 1.60% | 93.60% | 4.69% | 0.13% | NA |
| Tropical Japonica | 504 | 0.80% | 93.80% | 2.38% | 2.98% | NA |
| Japonica Intermediate | 241 | 1.70% | 88.80% | 9.54% | 0.00% | NA |
| VI/Aromatic | 96 | 33.30% | 34.40% | 13.54% | 18.75% | NA |
| Intermediate | 90 | 30.00% | 53.30% | 11.11% | 5.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620350630 | A -> G | LOC_Os06g35000.1 | missense_variant ; p.Lys235Glu; MODERATE | nonsynonymous_codon ; K235E | Average:11.625; most accessible tissue: Zhenshan97 panicle, score: 20.424 | benign  |
-1.285 |
TOLERATED | 1.00 |
| vg0620350630 | A -> DEL | LOC_Os06g35000.1 | N | frameshift_variant | Average:11.625; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0620350630 | NA | 1.96E-06 | mr1082 | 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 |
| vg0620350630 | 1.19E-06 | NA | mr1218 | 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 |
| vg0620350630 | NA | 8.23E-08 | mr1410 | 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 |
| vg0620350630 | NA | 1.83E-06 | mr1560 | 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 |
| vg0620350630 | NA | 1.21E-08 | mr1637 | 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 |
| vg0620350630 | NA | 8.91E-12 | mr1949 | 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 |