Search for Variation information by Variation ID:
Detailed information for vg1006617462:
| Variant ID: vg1006617462 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 6617462 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, C: 0.09, others allele: 0.00, population size: 90. )
Flanking Sequence (100 bp) in Reference Genome:
GTTGGAGTCTTGAAGTTCGGCGATCCGATCTCTCAAATCATGTTCAGTTTTCCTGGCAAGTTCCCTAGCTTCGTGCAGCTGGTTTCTGGTGGCCTCAAGG[G/C]
TTCCAAGGTGGGGAACTAACCTCTCAAGAGTCGCAGTTTTTGCTTCATTCCTGAGATGGATTCTCTGCAAAACAATTTTATTGGCATTTGAGCTAAGTGG
Reverse complement sequence
CCACTTAGCTCAAATGCCAATAAAATTGTTTTGCAGAGAATCCATCTCAGGAATGAAGCAAAAACTGCGACTCTTGAGAGGTTAGTTCCCCACCTTGGAA[C/G]
CCTTGAGGCCACCAGAAACCAGCTGCACGAAGCTAGGGAACTTGCCAGGAAAACTGAACATGATTTGAGAGATCGGATCGCCGAACTTCAAGACTCCAAC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 65.60% | 17.90% | 3.17% | 13.33% | NA |
| All Indica | 2759 | 60.10% | 29.50% | 4.71% | 5.69% | NA |
| All Japonica | 1512 | 68.20% | 0.80% | 1.06% | 29.96% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 85.50% | 8.40% | 4.37% | 1.68% | NA |
| Indica II | 465 | 37.60% | 47.70% | 5.81% | 8.82% | NA |
| Indica III | 913 | 59.70% | 29.80% | 5.59% | 4.93% | NA |
| Indica Intermediate | 786 | 54.50% | 34.50% | 3.31% | 7.76% | NA |
| Temperate Japonica | 767 | 93.00% | 0.30% | 0.00% | 6.78% | NA |
| Tropical Japonica | 504 | 27.60% | 0.40% | 2.58% | 69.44% | NA |
| Japonica Intermediate | 241 | 74.30% | 3.30% | 1.24% | 21.16% | NA |
| VI/Aromatic | 96 | 85.40% | 2.10% | 3.12% | 9.38% | NA |
| Intermediate | 90 | 72.20% | 14.40% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1006617462 | G -> C | LOC_Os10g11930.1 | missense_variant ; p.Thr433Ser; MODERATE | nonsynonymous_codon ; T433S | Average:19.281; most accessible tissue: Callus, score: 36.571 | benign  |
1.226 |
DELETERIOUS | 0.01 |
| vg1006617462 | G -> DEL | LOC_Os10g11930.1 | N | frameshift_variant | Average:19.281; most accessible tissue: Callus, score: 36.571 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1006617462 | NA | 7.14E-15 | mr1709 | 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 |
| vg1006617462 | NA | 1.12E-12 | mr1709 | 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 |
| vg1006617462 | 1.27E-08 | 2.83E-10 | mr1027_2 | 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 |
| vg1006617462 | NA | 1.75E-06 | mr1580_2 | 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 |
| vg1006617462 | NA | 4.02E-12 | mr1709_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 |
| vg1006617462 | NA | 1.94E-11 | mr1709_2 | 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 |
| vg1006617462 | NA | 1.02E-06 | mr1825_2 | 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 |