Search for Variation information by Variation ID:
Detailed information for vg0714877053:
| Variant ID: vg0714877053 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14877053 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGGCTCCCAACCTGCCTCATACATCTGCATGGGTGTTGAGGATGATGAACCTTCTTGTTCATTCCTTGCCATGTTGCGTGTCTCCCTGTATGTTCCACCT[G/A]
CACGAGATTCTTCTATGGTCCGCAGGGGAATGGTTAGTTCATGGCAGTTGTACAAATGATATCCCGCATTAGGCAACAGGATTTCATTTGTACAACCGGG
Reverse complement sequence
CCCGGTTGTACAAATGAAATCCTGTTGCCTAATGCGGGATATCATTTGTACAACTGCCATGAACTAACCATTCCCCTGCGGACCATAGAAGAATCTCGTG[C/T]
AGGTGGAACATACAGGGAGACACGCAACATGGCAAGGAATGAACAAGAAGGTTCATCATCCTCAACACCCATGCAGATGTATGAGGCAGGTTGGGAGCCA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.90% | 3.10% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 97.00% | 3.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Aus | 269 | 95.20% | 4.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 91.10% | 8.80% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 59.40% | 40.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0714877053 | G -> A | LOC_Os07g25910.1 | missense_variant ; p.Ala169Val; MODERATE | nonsynonymous_codon ; A169V | Average:35.677; most accessible tissue: Zhenshan97 root, score: 56.557 | benign  |
0.572 |
TOLERATED | 0.15 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714877053 | 8.21E-06 | 8.21E-06 | mr1738_2 | Ind_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 |
| vg0714877053 | 6.29E-06 | 2.77E-06 | mr1811_2 | Ind_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 |
| vg0714877053 | 2.89E-06 | 2.89E-06 | mr1832_2 | 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 |