Search for Variation information by Variation ID:
Detailed information for vg0138784720:
| Variant ID: vg0138784720 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 38784720 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCCAACGCATTGTCATCTGCTCCGGCAGCGTAGAGTACTGTGGAATAGACTTGAAGGAACTCCTCTCGGTCAGTGCTCCCATCATACTTTTCTATTGCTA[C/T]
AGGTCGGAATCTCTCAGGCCATCGGACATCACGCAGAGAACGACCGAAAGCCCTACACCCAGCGTTAGGGGCGGTGGATTGTCGGCGGTCGTGTGTCCTT
Reverse complement sequence
AAGGACACACGACCGCCGACAATCCACCGCCCCTAACGCTGGGTGTAGGGCTTTCGGTCGTTCTCTGCGTGATGTCCGATGGCCTGAGAGATTCCGACCT[G/A]
TAGCAATAGAAAAGTATGATGGGAGCACTGACCGAGAGGAGTTCCTTCAAGTCTATTCCACAGTACTCTACGCTGCCGGAGCAGATGACAATGCGTTGGC
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 | 98.60% | 0.90% | 0.49% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 95.80% | 2.70% | 1.52% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 91.70% | 5.30% | 3.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0138784720 | C -> T | LOC_Os01g66790.1 | missense_variant ; p.Val327Ile; MODERATE | nonsynonymous_codon ; V327I | Average:33.21; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 | benign  |
1.216 |
TOLERATED | 0.19 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0138784720 | 1.12E-06 | 1.12E-06 | mr1074_2 | Jap_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 |
| vg0138784720 | 1.71E-06 | 1.71E-06 | mr1081_2 | Jap_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 |
| vg0138784720 | NA | 1.92E-06 | mr1510_2 | 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 |
| vg0138784720 | NA | 8.71E-06 | mr1702_2 | 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 |