Search for Variation information by Variation ID:
Detailed information for vg1012357179:
| Variant ID: vg1012357179 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12357179 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 70. )
Flanking Sequence (100 bp) in Reference Genome:
CAGCGGAGGGTAATCCAAGTGATTACAAGGGCTGACCCACCAAGCCAGTTGTTCAAACGGCAGAAGAAGATGCAGATCCGTATGGTCCACAGCATCACTT[C/T]
GGCGGGTGAAGGGGCGCCGCAGTATCTGAACCAGCTAATTTCTTTTGGGCCGGAAGACGCGGAAGGAGTTATGTTCCCGCATCAAGATCCCCTGGTAATC
Reverse complement sequence
GATTACCAGGGGATCTTGATGCGGGAACATAACTCCTTCCGCGTCTTCCGGCCCAAAAGAAATTAGCTGGTTCAGATACTGCGGCGCCCCTTCACCCGCC[G/A]
AAGTGATGCTGTGGACCATACGGATCTGCATCTTCTTCTGCCGTTTGAACAACTGGCTTGGTGGGTCAGCCCTTGTAATCACTTGGATTACCCTCCGCTG
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 | 34.20% | 17.30% | 2.03% | 46.51% | NA |
| All Indica | 2759 | 6.70% | 28.00% | 2.17% | 63.07% | NA |
| All Japonica | 1512 | 89.40% | 0.30% | 0.86% | 9.39% | NA |
| Aus | 269 | 7.40% | 8.90% | 5.58% | 78.07% | NA |
| Indica I | 595 | 6.60% | 6.90% | 1.34% | 85.21% | NA |
| Indica II | 465 | 7.10% | 35.30% | 3.87% | 53.76% | NA |
| Indica III | 913 | 6.00% | 33.20% | 1.86% | 58.93% | NA |
| Indica Intermediate | 786 | 7.50% | 33.70% | 2.16% | 56.62% | NA |
| Temperate Japonica | 767 | 97.10% | 0.30% | 0.26% | 2.35% | NA |
| Tropical Japonica | 504 | 81.90% | 0.20% | 1.39% | 16.47% | NA |
| Japonica Intermediate | 241 | 80.50% | 0.80% | 1.66% | 17.01% | NA |
| VI/Aromatic | 96 | 15.60% | 1.00% | 7.29% | 76.04% | NA |
| Intermediate | 90 | 45.60% | 16.70% | 1.11% | 36.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012357179 | C -> T | LOC_Os10g24110.1 | missense_variant ; p.Ser385Leu; MODERATE | nonsynonymous_codon ; S385L | Average:12.416; most accessible tissue: Callus, score: 34.096 | benign  |
0.119 |
TOLERATED | 0.13 |
| vg1012357179 | C -> DEL | LOC_Os10g24110.1 | N | frameshift_variant | Average:12.416; most accessible tissue: Callus, score: 34.096 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1012357179 | NA | 3.91E-07 | mr1157 | 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 |
| vg1012357179 | NA | 9.25E-06 | mr1157 | 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 |
| vg1012357179 | NA | 1.70E-08 | mr1328 | 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 |
| vg1012357179 | NA | 3.57E-07 | mr1328 | 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 |
| vg1012357179 | NA | 9.02E-09 | mr1446 | 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 |
| vg1012357179 | NA | 1.11E-06 | mr1446 | 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 |
| vg1012357179 | 1.56E-07 | 3.62E-15 | mr1446_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 |
| vg1012357179 | 2.87E-06 | 5.79E-11 | mr1446_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 |