Search for Variation information by Variation ID:
Detailed information for vg1017279652:
| Variant ID: vg1017279652 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 17279652 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, C: 0.02, others allele: 0.00, population size: 123. )
Flanking Sequence (100 bp) in Reference Genome:
CGGCCCGAGTGCACTTGATGCTTCCGAAATTTTCGACAAGCTGAGAGTTGCTCCGGATATATATTTCAAGAACATCAAAGAAGCTGGAAGTATGGGAGTA[A/C]
GTATGGCGTTGGCGATGACTAAATCCCTTTATCCGAGAGTTGATATTGACGTCATTGATGGCTTTGCAGACGGGACGAGCGAAGAAGCTGCTCTTGACCT
Reverse complement sequence
AGGTCAAGAGCAGCTTCTTCGCTCGTCCCGTCTGCAAAGCCATCAATGACGTCAATATCAACTCTCGGATAAAGGGATTTAGTCATCGCCAACGCCATAC[T/G]
TACTCCCATACTTCCAGCTTCTTTGATGTTCTTGAAATATATATCCGGAGCAACTCTCAGCTTGTCGAAAATTTCGGAAGCATCAAGTGCACTCGGGCCG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 89.00% | 10.60% | 0.40% | 0.00% | NA |
| All Indica | 2759 | 93.20% | 6.10% | 0.69% | 0.00% | NA |
| All Japonica | 1512 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Aus | 269 | 8.60% | 91.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 88.70% | 9.20% | 2.08% | 0.00% | NA |
| Indica Intermediate | 786 | 93.10% | 6.90% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 34.40% | 65.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 12.20% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1017279652 | A -> C | LOC_Os10g33000.1 | missense_variant ; p.Ser627Arg; MODERATE | nonsynonymous_codon ; S627R | Average:25.117; most accessible tissue: Minghui63 panicle, score: 46.754 | benign  |
1.447 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1017279652 | 9.43E-06 | NA | mr1078_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 |
| vg1017279652 | 1.49E-06 | NA | mr1090_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 |
| vg1017279652 | 5.29E-08 | NA | mr1211_2 | 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 |