| Variant ID: vg0904077185 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 4077185 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGAAAAAACGGCGTTGGCCATGGCACCACACAAAACATACAGGAAGCTGCAAAAACCTGAAATAAATCGCTAGAATTTGACGGAGATCTGATAATCACAA[G/T]
CATACAAGAACATCTAAACCTCCTGTAAACCACTGAGTCCCATGTAGATCTGATTAGCAAAAGCTTACAACAAAGTTTAGATCCTTAGAGGTGGATTTCA
TGAAATCCACCTCTAAGGATCTAAACTTTGTTGTAAGCTTTTGCTAATCAGATCTACATGGGACTCAGTGGTTTACAGGAGGTTTAGATGTTCTTGTATG[C/A]
TTGTGATTATCAGATCTCCGTCAAATTCTAGCGATTTATTTCAGGTTTTTGCAGCTTCCTGTATGTTTTGTGTGGTGCCATGGCCAACGCCGTTTTTTCA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 73.00% | 12.50% | 12.29% | 2.22% | NA |
| All Indica | 2759 | 61.00% | 17.70% | 18.38% | 2.97% | NA |
| All Japonica | 1512 | 92.90% | 3.50% | 3.51% | 0.13% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 90.10% | 3.50% | 5.04% | 1.34% | NA |
| Indica II | 465 | 66.50% | 14.60% | 16.13% | 2.80% | NA |
| Indica III | 913 | 30.40% | 31.80% | 32.53% | 5.26% | NA |
| Indica Intermediate | 786 | 71.10% | 13.90% | 13.36% | 1.65% | NA |
| Temperate Japonica | 767 | 88.40% | 5.10% | 6.26% | 0.26% | NA |
| Tropical Japonica | 504 | 98.20% | 1.00% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.90% | 3.70% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 25.00% | 38.50% | 16.67% | 19.79% | NA |
| Intermediate | 90 | 80.00% | 13.30% | 4.44% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0904077185 | G -> DEL | N | N | silent_mutation | Average:49.406; most accessible tissue: Callus, score: 70.219 | N | N | N | N |
| vg0904077185 | G -> T | LOC_Os09g07940.1 | upstream_gene_variant ; 180.0bp to feature; MODIFIER | silent_mutation | Average:49.406; most accessible tissue: Callus, score: 70.219 | N | N | N | N |
| vg0904077185 | G -> T | LOC_Os09g07950.1 | upstream_gene_variant ; 4499.0bp to feature; MODIFIER | silent_mutation | Average:49.406; most accessible tissue: Callus, score: 70.219 | N | N | N | N |
| vg0904077185 | G -> T | LOC_Os09g07940-LOC_Os09g07950 | intergenic_region ; MODIFIER | silent_mutation | Average:49.406; most accessible tissue: Callus, score: 70.219 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0904077185 | NA | 6.18E-06 | mr1051_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 |
| vg0904077185 | NA | 7.20E-06 | mr1371_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 |
| vg0904077185 | 4.63E-06 | 8.52E-07 | mr1712_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 |