Search for Variation information by Variation ID:
Detailed information for vg0814573882:
| Variant ID: vg0814573882 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 14573882 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGCTCGGGGCGAACGTTAAAGTTCACGCTCCCGAACACTGTCTTCTTTGTTCCAGCTAGGGTAATCACCGTCTTCGAGTTCACGGTGGCAAAAAATATGG[C/T]
GCTGAAGAGCTCGGCGCTAGGCTCAAACCCGGAAGTCCGGCACGCCCAGTCAAAGATGGAGATCCGAATTAGTGCTGACAGGCTCAACTGTGGAAGCTCC
Reverse complement sequence
GGAGCTTCCACAGTTGAGCCTGTCAGCACTAATTCGGATCTCCATCTTTGACTGGGCGTGCCGGACTTCCGGGTTTGAGCCTAGCGCCGAGCTCTTCAGC[G/A]
CCATATTTTTTGCCACCGTGAACTCGAAGACGGTGATTACCCTAGCTGGAACAAAGAAGACAGTGTTCGGGAGCGTGAACTTTAACGTTCGCCCCGAGCG
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 | 54.80% | 0.10% | 7.96% | 37.16% | NA |
| All Indica | 2759 | 25.60% | 0.20% | 13.08% | 61.18% | NA |
| All Japonica | 1512 | 98.50% | 0.00% | 0.13% | 1.32% | NA |
| Aus | 269 | 86.60% | 0.00% | 3.35% | 10.04% | NA |
| Indica I | 595 | 15.60% | 0.00% | 9.75% | 74.62% | NA |
| Indica II | 465 | 21.50% | 0.00% | 18.49% | 60.00% | NA |
| Indica III | 913 | 29.80% | 0.30% | 13.58% | 56.30% | NA |
| Indica Intermediate | 786 | 30.50% | 0.30% | 11.83% | 57.38% | NA |
| Temperate Japonica | 767 | 98.00% | 0.00% | 0.26% | 1.69% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 74.40% | 0.00% | 4.44% | 21.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0814573882 | C -> T | LOC_Os08g24130.1 | missense_variant ; p.Ala103Thr; MODERATE | nonsynonymous_codon ; A103T | Average:21.119; most accessible tissue: Minghui63 root, score: 29.362 | benign  |
0.586 |
TOLERATED | 0.13 |
| vg0814573882 | C -> DEL | LOC_Os08g24130.1 | N | frameshift_variant | Average:21.119; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0814573882 | 1.59E-06 | NA | mr1158 | 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 |