Search for Variation information by Variation ID:
Detailed information for vg0622757624:
| Variant ID: vg0622757624 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 22757624 |
| Reference Allele: C | Alternative Allele: T,G |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, T: 0.18, others allele: 0.00, population size: 100. )
Flanking Sequence (100 bp) in Reference Genome:
CATCAAAAGGTAATCTTCTAGATCTGTCCCATTAATTTACGCTGTCATAACTGTATCCTCAACCATTTGGATTTCAAACAGCGCAAGCCACCAGGATGGC[C/T,G]
CAAATGGAGAAACAAATTGAAGCCTTGAAAAGAGACAAGGTAGAACTGGCTGCACAAAGGGACTCGGCCTTGAAGGAGATTGAAGGTACTGCCAGCTAAC
Reverse complement sequence
GTTAGCTGGCAGTACCTTCAATCTCCTTCAAGGCCGAGTCCCTTTGTGCAGCCAGTTCTACCTTGTCTCTTTTCAAGGCTTCAATTTGTTTCTCCATTTG[G/A,C]
GCCATCCTGGTGGCTTGCGCTGTTTGAAATCCAAATGGTTGAGGATACAGTTATGACAGCGTAAATTAATGGGACAGATCTAGAAGATTACCTTTTGATG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 52.30% | 20.10% | 14.11% | 10.75% | G: 2.71% |
| All Indica | 2759 | 60.80% | 9.00% | 16.82% | 8.77% | G: 4.60% |
| All Japonica | 1512 | 42.90% | 34.40% | 7.94% | 14.81% | NA |
| Aus | 269 | 34.20% | 27.90% | 25.65% | 12.27% | NA |
| Indica I | 595 | 77.30% | 1.80% | 6.05% | 10.08% | G: 4.71% |
| Indica II | 465 | 57.20% | 7.30% | 20.00% | 9.89% | G: 5.59% |
| Indica III | 913 | 50.40% | 14.80% | 22.89% | 7.23% | G: 4.71% |
| Indica Intermediate | 786 | 62.60% | 8.70% | 16.03% | 8.91% | G: 3.82% |
| Temperate Japonica | 767 | 65.30% | 12.30% | 6.39% | 16.04% | NA |
| Tropical Japonica | 504 | 15.50% | 67.30% | 9.92% | 7.34% | NA |
| Japonica Intermediate | 241 | 28.60% | 36.10% | 8.71% | 26.56% | NA |
| VI/Aromatic | 96 | 9.40% | 87.50% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 52.20% | 24.40% | 12.22% | 10.00% | G: 1.11% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0622757624 | C -> G | LOC_Os06g38410.1 | synonymous_variant ; p.Ala568Ala; LOW | synonymous_codon | Average:12.481; most accessible tissue: Zhenshan97 root, score: 22.162 | N | N | N | N |
| vg0622757624 | C -> G | LOC_Os06g38410.1 | synonymous_variant ; p.Ala568Ala; LOW | nonsynonymous_codon ; A568E | Average:12.481; most accessible tissue: Zhenshan97 root, score: 22.162 | possibly damaging  |
1.751 |
TOLERATED | 0.07 |
| vg0622757624 | C -> T | LOC_Os06g38410.1 | synonymous_variant ; p.Ala568Ala; LOW | synonymous_codon | Average:12.481; most accessible tissue: Zhenshan97 root, score: 22.162 | N | N | N | N |
| vg0622757624 | C -> DEL | LOC_Os06g38410.1 | N | frameshift_variant | Average:12.481; most accessible tissue: Zhenshan97 root, score: 22.162 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0622757624 | NA | 4.61E-10 | mr1825 | 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 |
| vg0622757624 | NA | 9.32E-13 | mr1178_2 | Jap_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 |