| Variant ID: vg0713647697 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 13647697 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 241. )
GATAGCTGTGCTCAACATCGACATCTTCATCGAGACATGAGGAGTGATCAACATAACCTTTATGAGGTAAGTGACGATGTTCTAGGTAAGATCAAATCTG[C/T]
ACTGCCTTATTTCGAGGGAAACTATGATCTTCATGCTTACATTAATTGGGAGCTAGCGGTTGATAGTGAATTTCAAAAGCATGTCTTGTCTGAGAAACAA
TTGTTTCTCAGACAAGACATGCTTTTGAAATTCACTATCAACCGCTAGCTCCCAATTAATGTAAGCATGAAGATCATAGTTTCCCTCGAAATAAGGCAGT[G/A]
CAGATTTGATCTTACCTAGAACATCGTCACTTACCTCATAAAGGTTATGTTGATCACTCCTCATGTCTCGATGAAGATGTCGATGTTGAGCACAGCTATC
| 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 | 77.10% | 20.70% | 0.57% | 1.57% | NA |
| All Indica | 2759 | 73.00% | 26.60% | 0.33% | 0.04% | NA |
| All Japonica | 1512 | 98.80% | 0.70% | 0.07% | 0.40% | NA |
| Aus | 269 | 19.00% | 77.30% | 2.23% | 1.49% | NA |
| Indica I | 595 | 73.60% | 26.40% | 0.00% | 0.00% | NA |
| Indica II | 465 | 89.50% | 10.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 62.80% | 36.80% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 74.70% | 24.60% | 0.64% | 0.13% | NA |
| Temperate Japonica | 767 | 99.60% | 0.30% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 99.20% | 0.40% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 95.40% | 2.90% | 0.41% | 1.24% | NA |
| VI/Aromatic | 96 | 12.50% | 14.60% | 11.46% | 61.46% | NA |
| Intermediate | 90 | 83.30% | 12.20% | 0.00% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0713647697 | C -> DEL | N | N | silent_mutation | Average:15.366; most accessible tissue: Callus, score: 25.734 | N | N | N | N |
| vg0713647697 | C -> T | LOC_Os07g24060.1 | downstream_gene_variant ; 1583.0bp to feature; MODIFIER | silent_mutation | Average:15.366; most accessible tissue: Callus, score: 25.734 | N | N | N | N |
| vg0713647697 | C -> T | LOC_Os07g24080.1 | downstream_gene_variant ; 3360.0bp to feature; MODIFIER | silent_mutation | Average:15.366; most accessible tissue: Callus, score: 25.734 | N | N | N | N |
| vg0713647697 | C -> T | LOC_Os07g24070.1 | intron_variant ; MODIFIER | silent_mutation | Average:15.366; most accessible tissue: Callus, score: 25.734 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0713647697 | 7.94E-06 | 3.57E-10 | mr1027_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 |
| vg0713647697 | NA | 5.05E-07 | mr1063_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 |
| vg0713647697 | NA | 4.42E-06 | mr1825_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 |