Search for Variation information by Variation ID:
Detailed information for vg1209224096:
| Variant ID: vg1209224096 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9224096 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 209. )
Flanking Sequence (100 bp) in Reference Genome:
CCAAAGTCTATGAGCACCATATTTGTCTTGATGAGATCCTCGGCATTTCTACCCAACTTCTTGAACGTAGCAAAAGGCATCAAATTTACCGCGGCCCCAC[T/C]
ATCAACCATCATTTTAGACATCGGCTTCCCATTGACATAGCCGTTTATATACAATGGTTTAAGATGCCGATTCTCTGTCCCCTCAGGTTTCTCGAACACT
Reverse complement sequence
AGTGTTCGAGAAACCTGAGGGGACAGAGAATCGGCATCTTAAACCATTGTATATAAACGGCTATGTCAATGGGAAGCCGATGTCTAAAATGATGGTTGAT[A/G]
GTGGGGCCGCGGTAAATTTGATGCCTTTTGCTACGTTCAAGAAGTTGGGTAGAAATGCCGAGGATCTCATCAAGACAAATATGGTGCTCATAGACTTTGG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.80% | 32.50% | 0.85% | 31.78% | NA |
| All Indica | 2759 | 5.10% | 43.00% | 1.30% | 50.53% | NA |
| All Japonica | 1512 | 94.00% | 1.70% | 0.20% | 4.10% | NA |
| Aus | 269 | 4.10% | 95.20% | 0.00% | 0.74% | NA |
| Indica I | 595 | 3.90% | 53.90% | 0.34% | 41.85% | NA |
| Indica II | 465 | 11.60% | 40.90% | 0.65% | 46.88% | NA |
| Indica III | 913 | 2.10% | 35.90% | 2.30% | 59.69% | NA |
| Indica Intermediate | 786 | 5.90% | 44.30% | 1.27% | 48.60% | NA |
| Temperate Japonica | 767 | 93.10% | 0.80% | 0.26% | 5.87% | NA |
| Tropical Japonica | 504 | 93.80% | 2.80% | 0.20% | 3.17% | NA |
| Japonica Intermediate | 241 | 97.10% | 2.50% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 25.00% | 41.70% | 1.04% | 32.29% | NA |
| Intermediate | 90 | 54.40% | 31.10% | 0.00% | 14.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209224096 | T -> C | LOC_Os12g16150.1 | missense_variant ; p.Ser541Gly; MODERATE | nonsynonymous_codon ; S541G | Average:25.878; most accessible tissue: Minghui63 flag leaf, score: 41.254 | benign  |
-1.044 |
TOLERATED | 1.00 |
| vg1209224096 | T -> DEL | LOC_Os12g16150.1 | N | frameshift_variant | Average:25.878; most accessible tissue: Minghui63 flag leaf, score: 41.254 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1209224096 | NA | 3.98E-07 | mr1425 | 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 |
| vg1209224096 | NA | 1.94E-06 | mr1425_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 |
| vg1209224096 | 3.93E-06 | 3.93E-06 | mr1584_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 |
| vg1209224096 | NA | 3.44E-06 | mr1864_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 |