| Variant ID: vg0706617703 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 6617703 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TCGCCGGGATGCTCCTCGAGGAGCCGTCGACACATGCCACCCTGCTGGGACACACTGAAGGTCCCCAGAGCAGCCGCGGACACCGTCGAGGTGCTCGTAC[A/G]
CCGTCGTCAAGTCCAGCTGTGATTCTTTCACTTCATCACGGCGGAGTTGTCATGTCGACTGATCTGTTGGCGCTGATCGCAAGCCTCCGTCAAGATCGAT
ATCGATCTTGACGGAGGCTTGCGATCAGCGCCAACAGATCAGTCGACATGACAACTCCGCCGTGATGAAGTGAAAGAATCACAGCTGGACTTGACGACGG[T/C]
GTACGAGCACCTCGACGGTGTCCGCGGCTGCTCTGGGGACCTTCAGTGTGTCCCAGCAGGGTGGCATGTGTCGACGGCTCCTCGAGGAGCATCCCGGCGA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 38.90% | 5.90% | 3.09% | 52.14% | NA |
| All Indica | 2759 | 9.70% | 9.90% | 4.53% | 75.82% | NA |
| All Japonica | 1512 | 93.00% | 0.10% | 0.66% | 6.28% | NA |
| Aus | 269 | 6.30% | 0.70% | 2.97% | 89.96% | NA |
| Indica I | 595 | 12.80% | 24.50% | 3.03% | 59.66% | NA |
| Indica II | 465 | 13.80% | 2.60% | 4.52% | 79.14% | NA |
| Indica III | 913 | 3.40% | 8.80% | 3.94% | 83.90% | NA |
| Indica Intermediate | 786 | 12.50% | 4.50% | 6.36% | 76.72% | NA |
| Temperate Japonica | 767 | 87.50% | 0.00% | 1.17% | 11.34% | NA |
| Tropical Japonica | 504 | 99.40% | 0.20% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.41% | 2.49% | NA |
| VI/Aromatic | 96 | 93.80% | 0.00% | 0.00% | 6.25% | NA |
| Intermediate | 90 | 62.20% | 2.20% | 3.33% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0706617703 | A -> DEL | N | N | silent_mutation | Average:12.983; most accessible tissue: Callus, score: 61.282 | N | N | N | N |
| vg0706617703 | A -> G | LOC_Os07g11920.1 | upstream_gene_variant ; 3941.0bp to feature; MODIFIER | silent_mutation | Average:12.983; most accessible tissue: Callus, score: 61.282 | N | N | N | N |
| vg0706617703 | A -> G | LOC_Os07g11920-LOC_Os07g11970 | intergenic_region ; MODIFIER | silent_mutation | Average:12.983; most accessible tissue: Callus, score: 61.282 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0706617703 | NA | 6.67E-09 | mr1565 | 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 |
| vg0706617703 | NA | 1.71E-07 | mr1715 | 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 |
| vg0706617703 | NA | 9.96E-08 | mr1771 | 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 |