Search for Variation information by Variation ID:
Detailed information for vg1121600548:
| Variant ID: vg1121600548 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 21600548 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATTATAATGGCACTAGTGGCACATTATGATTTGGAATTACATCAGATGGATGTAAAAACGACATTTCTAAATGGAGATTTGGAGGAAAAAGTATACATGG[C/T]
GCAACCGAAAGGTTTTGTCATGAAAGGAAACGGAAATATGGGATGTCGTCTAAAGAGATCCATTTATGAATTAAAGCAAGCTTCGAGACAGTGGTACTTG
Reverse complement sequence
CAAGTACCACTGTCTCGAAGCTTGCTTTAATTCATAAATGGATCTCTTTAGACGACATCCCATATTTCCGTTTCCTTTCATGACAAAACCTTTCGGTTGC[G/A]
CCATGTATACTTTTTCCTCCAAATCTCCATTTAGAAATGTCGTTTTTACATCCATCTGATGTAATTCCAAATCATAATGTGCCACTAGTGCCATTATAAT
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 | 70.30% | 0.20% | 23.59% | 5.88% | NA |
| All Indica | 2759 | 66.80% | 0.40% | 30.63% | 2.14% | NA |
| All Japonica | 1512 | 77.10% | 0.00% | 10.45% | 12.50% | NA |
| Aus | 269 | 79.20% | 0.00% | 20.45% | 0.37% | NA |
| Indica I | 595 | 78.20% | 0.80% | 16.30% | 4.71% | NA |
| Indica II | 465 | 60.60% | 0.00% | 36.56% | 2.80% | NA |
| Indica III | 913 | 61.20% | 0.20% | 37.90% | 0.66% | NA |
| Indica Intermediate | 786 | 68.40% | 0.50% | 29.52% | 1.53% | NA |
| Temperate Japonica | 767 | 87.50% | 0.00% | 4.17% | 8.34% | NA |
| Tropical Japonica | 504 | 62.70% | 0.00% | 18.65% | 18.65% | NA |
| Japonica Intermediate | 241 | 73.90% | 0.00% | 13.28% | 12.86% | NA |
| VI/Aromatic | 96 | 35.40% | 0.00% | 40.62% | 23.96% | NA |
| Intermediate | 90 | 73.30% | 0.00% | 20.00% | 6.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1121600548 | C -> T | LOC_Os11g36590.1 | missense_variant ; p.Ala780Val; MODERATE | nonsynonymous_codon ; A780V | Average:7.739; most accessible tissue: Callus, score: 20.827 | benign  |
0.23 |
TOLERATED | 0.41 |
| vg1121600548 | C -> DEL | LOC_Os11g36590.1 | N | frameshift_variant | Average:7.739; most accessible tissue: Callus, score: 20.827 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1121600548 | 1.68E-06 | 4.22E-06 | mr1336 | 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 |