| Variant ID: vg0709361289 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 9361289 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AACCGGCCGAAGCACTGCTCGCCGAACGTTGAAACCGTGACAGCTCGTTTTCGGAAAACATACCGATCGTCGCTATACTCGACTTATGCAAATACTTAAG[C/T]
GTTTCTGGACGCGTATGCCAAAAGTCGAGAGCGAATGATGAGGGCTGAAAAATCGACAAATCTTTTCGCTAAATTACGCAAAGGGGCCGACATGTTTCGA
TCGAAACATGTCGGCCCCTTTGCGTAATTTAGCGAAAAGATTTGTCGATTTTTCAGCCCTCATCATTCGCTCTCGACTTTTGGCATACGCGTCCAGAAAC[G/A]
CTTAAGTATTTGCATAAGTCGAGTATAGCGACGATCGGTATGTTTTCCGAAAACGAGCTGTCACGGTTTCAACGTTCGGCGAGCAGTGCTTCGGCCGGTT
| 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 | 84.70% | 5.40% | 2.96% | 6.92% | NA |
| All Indica | 2759 | 74.30% | 9.20% | 4.89% | 11.56% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.07% | NA |
| Aus | 269 | 99.30% | 0.40% | 0.00% | 0.37% | NA |
| Indica I | 595 | 71.10% | 1.00% | 6.55% | 21.34% | NA |
| Indica II | 465 | 76.30% | 8.40% | 5.81% | 9.46% | NA |
| Indica III | 913 | 71.90% | 16.00% | 3.61% | 8.54% | NA |
| Indica Intermediate | 786 | 78.40% | 8.10% | 4.58% | 8.91% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 88.90% | 1.10% | 4.44% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0709361289 | C -> DEL | N | N | silent_mutation | Average:6.537; most accessible tissue: Callus, score: 22.369 | N | N | N | N |
| vg0709361289 | C -> T | LOC_Os07g16040.1 | downstream_gene_variant ; 3500.0bp to feature; MODIFIER | silent_mutation | Average:6.537; most accessible tissue: Callus, score: 22.369 | N | N | N | N |
| vg0709361289 | C -> T | LOC_Os07g16054.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.537; most accessible tissue: Callus, score: 22.369 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0709361289 | NA | 2.82E-07 | mr1841 | 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 |
| vg0709361289 | NA | 4.69E-06 | mr1238_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 |
| vg0709361289 | 2.70E-06 | 2.70E-06 | mr1945_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 |