Search for Variation information by Variation ID:
Detailed information for vg0617687728:
| Variant ID: vg0617687728 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 17687728 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTGGCGAAGAACAAGGGCACGCGGAGATCATGAGAGCTTTGTCCCAAATTCGGAGAAAGAGATGCTGTGGACCACAATGCTCGAGACATTCACCCTTCCC[A/G]
CGGGTACAGAGGACAAAGTGAAAAGGTGGACTCTAAAGAAAATGGCAGAACAGTTTCAGAGCTTCAAGGGAGAGCTGTACAAGAAATATATCCTGAAGGG
Reverse complement sequence
CCCTTCAGGATATATTTCTTGTACAGCTCTCCCTTGAAGCTCTGAAACTGTTCTGCCATTTTCTTTAGAGTCCACCTTTTCACTTTGTCCTCTGTACCCG[T/C]
GGGAAGGGTGAATGTCTCGAGCATTGTGGTCCACAGCATCTCTTTCTCCGAATTTGGGACAAAGCTCTCATGATCTCCGCGTGCCCTTGTTCTTCGCCAG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.70% | 3.50% | 5.56% | 0.25% | NA |
| All Indica | 2759 | 95.60% | 0.70% | 3.23% | 0.43% | NA |
| All Japonica | 1512 | 79.60% | 9.40% | 11.04% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.60% | 0.30% | 2.35% | 0.67% | NA |
| Indica II | 465 | 95.70% | 0.60% | 2.80% | 0.86% | NA |
| Indica III | 913 | 96.80% | 0.80% | 2.30% | 0.11% | NA |
| Indica Intermediate | 786 | 93.40% | 1.00% | 5.22% | 0.38% | NA |
| Temperate Japonica | 767 | 98.20% | 0.70% | 1.17% | 0.00% | NA |
| Tropical Japonica | 504 | 50.80% | 22.80% | 26.39% | 0.00% | NA |
| Japonica Intermediate | 241 | 80.50% | 9.10% | 10.37% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 2.20% | 7.78% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0617687728 | A -> G | LOC_Os06g30570.1 | missense_variant ; p.Thr181Ala; MODERATE | nonsynonymous_codon ; T181A | Average:14.946; most accessible tissue: Minghui63 root, score: 21.615 | benign  |
-0.715 |
TOLERATED | 1.00 |
| vg0617687728 | A -> DEL | LOC_Os06g30570.1 | N | frameshift_variant | Average:14.946; most accessible tissue: Minghui63 root, score: 21.615 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0617687728 | NA | 6.33E-07 | mr1206 | 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 |
| vg0617687728 | NA | 2.61E-08 | mr1229 | 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 |
| vg0617687728 | NA | 6.20E-08 | mr1518 | Jap_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 |
| vg0617687728 | NA | 3.60E-08 | mr1596 | 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 |
| vg0617687728 | NA | 3.56E-07 | mr1723 | Jap_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 |
| vg0617687728 | NA | 6.77E-08 | mr1880 | 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 |