Search for Variation information by Variation ID:
Detailed information for vg1208769199:
| Variant ID: vg1208769199 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 8769199 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGGTCATTCAAGGACCGATAACAAGAGCTCGTGCGCGACAATTAAATTTAGAGGTGAGCTCGTTCCTATGTTCTTCTTTGTATGAATTCGAGAATAGATT[G/T]
CTACCTAATGATTATATTGTGCTTTGGAACAATGGAGGGGACAAGGAGACACTAGGAGAAGGACTTACAGCCATGGAGGATCATCGGGGATGTTCAAGTC
Reverse complement sequence
GACTTGAACATCCCCGATGATCCTCCATGGCTGTAAGTCCTTCTCCTAGTGTCTCCTTGTCCCCTCCATTGTTCCAAAGCACAATATAATCATTAGGTAG[C/A]
AATCTATTCTCGAATTCATACAAAGAAGAACATAGGAACGAGCTCACCTCTAAATTTAATTGTCGCGCACGAGCTCTTGTTATCGGTCCTTGAATGACCG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 67.40% | 3.30% | 27.82% | 1.46% | NA |
| All Indica | 2759 | 52.10% | 5.30% | 40.41% | 2.21% | NA |
| All Japonica | 1512 | 97.80% | 0.40% | 1.79% | 0.07% | NA |
| Aus | 269 | 40.90% | 1.50% | 55.02% | 2.60% | NA |
| Indica I | 595 | 47.60% | 4.40% | 46.05% | 2.02% | NA |
| Indica II | 465 | 53.10% | 6.00% | 38.49% | 2.37% | NA |
| Indica III | 913 | 53.50% | 5.80% | 38.55% | 2.19% | NA |
| Indica Intermediate | 786 | 53.40% | 4.80% | 39.44% | 2.29% | NA |
| Temperate Japonica | 767 | 97.40% | 0.70% | 1.83% | 0.13% | NA |
| Tropical Japonica | 504 | 97.80% | 0.20% | 1.98% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 87.50% | 1.00% | 11.46% | 0.00% | NA |
| Intermediate | 90 | 82.20% | 2.20% | 15.56% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1208769199 | G -> DEL | LOC_Os12g15350.1 | N | frameshift_variant | Average:17.316; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |
| vg1208769199 | G -> T | LOC_Os12g15350.1 | missense_variant ; p.Leu1148Phe; MODERATE | nonsynonymous_codon ; L1148F | Average:17.316; most accessible tissue: Minghui63 root, score: 29.362 | benign  |
0.23 |
TOLERATED | 0.26 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1208769199 | 1.34E-06 | 1.34E-06 | mr1582 | 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 |
| vg1208769199 | NA | 3.43E-06 | mr1772 | 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 |