Search for Variation information by Variation ID:
Detailed information for vg0509902421:
| Variant ID: vg0509902421 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 9902421 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 99. )
Flanking Sequence (100 bp) in Reference Genome:
TATGTTTCTCGGTTTTGGGCACTTGTCGGCGAAATGACCCATTCCTTGACAATTGAAGCAACAGATGTCTTCCCGGACTCGGCATTTTCTTTTCTCATTT[C/T]
GATTCCTCTGTCCTGGCACTGGAGTTAGGCTGAAACTGTGATCTTGGCGGGGATTTGTGTTGCCTTGATGCTTCTCTCCGTTGGAACTGGCGGGTTGGTT
Reverse complement sequence
AACCAACCCGCCAGTTCCAACGGAGAGAAGCATCAAGGCAACACAAATCCCCGCCAAGATCACAGTTTCAGCCTAACTCCAGTGCCAGGACAGAGGAATC[G/A]
AAATGAGAAAAGAAAATGCCGAGTCCGGGAAGACATCTGTTGCTTCAATTGTCAAGGAATGGGTCATTTCGCCGACAAGTGCCCAAAACCGAGAAACATA
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 | 73.00% | 13.60% | 7.72% | 5.71% | NA |
| All Indica | 2759 | 63.70% | 21.30% | 9.64% | 5.29% | NA |
| All Japonica | 1512 | 98.70% | 0.40% | 0.86% | 0.00% | NA |
| Aus | 269 | 11.90% | 15.20% | 28.25% | 44.61% | NA |
| Indica I | 595 | 82.90% | 8.70% | 6.22% | 2.18% | NA |
| Indica II | 465 | 75.10% | 21.30% | 2.58% | 1.08% | NA |
| Indica III | 913 | 46.20% | 28.70% | 15.66% | 9.42% | NA |
| Indica Intermediate | 786 | 62.80% | 22.40% | 9.41% | 5.34% | NA |
| Temperate Japonica | 767 | 98.60% | 0.40% | 1.04% | 0.00% | NA |
| Tropical Japonica | 504 | 99.00% | 0.40% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 2.10% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 83.30% | 5.60% | 7.78% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0509902421 | C -> T | LOC_Os05g17280.1 | missense_variant ; p.Arg210Gln; MODERATE | nonsynonymous_codon ; R210Q | Average:20.279; most accessible tissue: Zhenshan97 flag leaf, score: 31.305 | benign  |
1.092 |
TOLERATED | 1.00 |
| vg0509902421 | C -> DEL | LOC_Os05g17280.1 | N | frameshift_variant | Average:20.279; most accessible tissue: Zhenshan97 flag leaf, score: 31.305 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0509902421 | NA | 3.15E-06 | mr1015 | 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 |
| vg0509902421 | NA | 2.80E-06 | mr1532 | 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 |
| vg0509902421 | NA | 3.62E-06 | mr1677 | 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 |
| vg0509902421 | 4.55E-06 | 1.09E-07 | mr1678 | 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 |
| vg0509902421 | NA | 2.13E-06 | mr1555_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 |