| Variant ID: vg0308974609 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 8974609 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTCGTCTCCGCCCCCGAGGCCAGCTCGAGCCCATCGCAGCGGCCTCACACCGCCCTCTGGTGATGTAGTTCGACGGCACCTGTAGGAACCGGCCCCACCT[A/G]
TCACCAGGCCTTAGGAAGTGGCGTTACGCCCGACCGCTTCCCTCGAGGAGGGCGATCGCCCTGGCATAACGCCGGGGGCTACTGTCGGTGACATGGGACC
GGTCCCATGTCACCGACAGTAGCCCCCGGCGTTATGCCAGGGCGATCGCCCTCCTCGAGGGAAGCGGTCGGGCGTAACGCCACTTCCTAAGGCCTGGTGA[T/C]
AGGTGGGGCCGGTTCCTACAGGTGCCGTCGAACTACATCACCAGAGGGCGGTGTGAGGCCGCTGCGATGGGCTCGAGCTGGCCTCGGGGGCGGAGACGAG
| 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 | 44.80% | 5.10% | 3.94% | 46.17% | NA |
| All Indica | 2759 | 27.60% | 1.10% | 2.28% | 69.08% | NA |
| All Japonica | 1512 | 77.40% | 13.80% | 7.61% | 1.19% | NA |
| Aus | 269 | 21.20% | 0.00% | 1.12% | 77.70% | NA |
| Indica I | 595 | 65.90% | 0.20% | 1.68% | 32.27% | NA |
| Indica II | 465 | 9.20% | 0.60% | 1.51% | 88.60% | NA |
| Indica III | 913 | 15.10% | 1.40% | 1.10% | 82.37% | NA |
| Indica Intermediate | 786 | 23.90% | 1.50% | 4.58% | 69.97% | NA |
| Temperate Japonica | 767 | 61.10% | 26.50% | 11.47% | 0.91% | NA |
| Tropical Japonica | 504 | 94.40% | 0.00% | 3.97% | 1.59% | NA |
| Japonica Intermediate | 241 | 93.80% | 2.10% | 2.90% | 1.24% | NA |
| VI/Aromatic | 96 | 84.40% | 0.00% | 0.00% | 15.62% | NA |
| Intermediate | 90 | 54.40% | 2.20% | 5.56% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0308974609 | A -> DEL | N | N | silent_mutation | Average:27.814; most accessible tissue: Zhenshan97 flag leaf, score: 72.757 | N | N | N | N |
| vg0308974609 | A -> G | LOC_Os03g16280.1 | downstream_gene_variant ; 38.0bp to feature; MODIFIER | silent_mutation | Average:27.814; most accessible tissue: Zhenshan97 flag leaf, score: 72.757 | N | N | N | N |
| vg0308974609 | A -> G | LOC_Os03g16280-LOC_Os03g16290 | intergenic_region ; MODIFIER | silent_mutation | Average:27.814; most accessible tissue: Zhenshan97 flag leaf, score: 72.757 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0308974609 | 9.71E-06 | 9.71E-06 | mr1168 | 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 |
| vg0308974609 | 8.41E-06 | NA | mr1757 | 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 |
| vg0308974609 | 4.00E-07 | NA | mr1403_2 | 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 |
| vg0308974609 | NA | 3.80E-07 | mr1915_2 | 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 |