Search for Variation information by Variation ID:
Detailed information for vg0209217731:
| Variant ID: vg0209217731 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 9217731 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATTAATTATTCTGTACAATAATTAATAGAAACATAGTGAAAAAACCAAACCTAGATCTTCATCTTGCTGAACTCTTTTTGTCCATTGTGCAAGTTTCTTC[C/T]
GGTTCATTCGCATTTTCCTTGGTTGGCTACCCCTAGGATCCACAAAATCAAGGCCGGAAATCTGTCTCACAAATTTCGTGACCAAACCTGAAAACCCTTC
Reverse complement sequence
GAAGGGTTTTCAGGTTTGGTCACGAAATTTGTGAGACAGATTTCCGGCCTTGATTTTGTGGATCCTAGGGGTAGCCAACCAAGGAAAATGCGAATGAACC[G/A]
GAAGAAACTTGCACAATGGACAAAAAGAGTTCAGCAAGATGAAGATCTAGGTTTGGTTTTTTCACTATGTTTCTATTAATTATTGTACAGAATAATTAAT
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 | 45.70% | 34.00% | 13.80% | 6.45% | NA |
| All Indica | 2759 | 18.30% | 57.00% | 20.33% | 4.42% | NA |
| All Japonica | 1512 | 97.90% | 0.80% | 0.53% | 0.73% | NA |
| Aus | 269 | 12.30% | 4.50% | 24.16% | 59.11% | NA |
| Indica I | 595 | 43.50% | 21.80% | 30.76% | 3.87% | NA |
| Indica II | 465 | 14.80% | 77.20% | 3.23% | 4.73% | NA |
| Indica III | 913 | 2.50% | 71.40% | 23.33% | 2.74% | NA |
| Indica Intermediate | 786 | 19.50% | 54.80% | 19.08% | 6.62% | NA |
| Temperate Japonica | 767 | 98.30% | 0.70% | 0.26% | 0.78% | NA |
| Tropical Japonica | 504 | 97.20% | 1.00% | 0.79% | 0.99% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.80% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 8.33% | 4.17% | NA |
| Intermediate | 90 | 64.40% | 14.40% | 11.11% | 10.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0209217731 | C -> T | LOC_Os02g16220.1 | missense_variant ; p.Arg503Gln; MODERATE | nonsynonymous_codon ; R503Q | Average:14.749; most accessible tissue: Minghui63 flag leaf, score: 28.142 | benign  |
0.383 |
TOLERATED | 0.53 |
| vg0209217731 | C -> DEL | LOC_Os02g16220.1 | N | frameshift_variant | Average:14.749; most accessible tissue: Minghui63 flag leaf, score: 28.142 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0209217731 | NA | 8.96E-11 | mr1281 | 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 |
| vg0209217731 | NA | 2.44E-16 | mr1040_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 |
| vg0209217731 | 4.76E-06 | NA | mr1167_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 |
| vg0209217731 | NA | 3.42E-20 | mr1362_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 |