Search for Variation information by Variation ID:
Detailed information for vg0714360090:
| Variant ID: vg0714360090 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14360090 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CACTCCGTTTTTGTGGGATCAAACGGGAGAACGTCAGGTTTTCGGGACTGATATCTTAAGGGAAGCAGAAGAGAAGGTAAAGATCATTCAAGAAAGATTG[C/T]
GTATAGCTCAGTCTCGTCATAAGAGTTATGCCGACAATCGCCGCAGAGATTTAAGTTTTGAGGAAGGAGATCATGTGTACCTTCGTGTCACGCCTCTTCG
Reverse complement sequence
CGAAGAGGCGTGACACGAAGGTACACATGATCTCCTTCCTCAAAACTTAAATCTCTGCGGCGATTGTCGGCATAACTCTTATGACGAGACTGAGCTATAC[G/A]
CAATCTTTCTTGAATGATCTTTACCTTCTCTTCTGCTTCCCTTAAGATATCAGTCCCGAAAACCTGACGTTCTCCCGTTTGATCCCACAAAAACGGAGTG
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 | 80.00% | 0.20% | 2.18% | 17.58% | NA |
| All Indica | 2759 | 73.10% | 0.40% | 3.01% | 23.52% | NA |
| All Japonica | 1512 | 88.60% | 0.00% | 1.19% | 10.19% | NA |
| Aus | 269 | 97.40% | 0.00% | 0.00% | 2.60% | NA |
| Indica I | 595 | 69.70% | 0.50% | 1.51% | 28.24% | NA |
| Indica II | 465 | 74.20% | 0.00% | 2.80% | 23.01% | NA |
| Indica III | 913 | 71.00% | 0.50% | 4.27% | 24.21% | NA |
| Indica Intermediate | 786 | 77.50% | 0.30% | 2.80% | 19.47% | NA |
| Temperate Japonica | 767 | 89.20% | 0.00% | 0.78% | 10.04% | NA |
| Tropical Japonica | 504 | 94.40% | 0.00% | 1.19% | 4.37% | NA |
| Japonica Intermediate | 241 | 74.70% | 0.00% | 2.49% | 22.82% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 80.00% | 0.00% | 2.22% | 17.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0714360090 | C -> DEL | LOC_Os07g25130.1 | N | frameshift_variant | Average:14.681; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0714360090 | C -> T | LOC_Os07g25130.1 | missense_variant ; p.Arg957Cys; MODERATE | nonsynonymous_codon ; R957C | Average:14.681; most accessible tissue: Minghui63 panicle, score: 20.733 | benign  |
1.155 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714360090 | NA | 1.29E-06 | mr1316 | 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 |
| vg0714360090 | NA | 5.78E-06 | mr1716 | 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 |
| vg0714360090 | NA | 2.78E-06 | mr1749 | 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 |
| vg0714360090 | NA | 2.65E-06 | mr1821 | 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 |