| Variant ID: vg0403131494 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 3131494 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GGGGATTACGCGTTTGACAGAGATGGGAGGCGGGGATCGATCTGGACCGTTCGGTTTTCACAGGATGAATCTGATCTATTGAGTGATGAATGAAAGAATG[A/G]
AAGGATGAGTGAAAGTATTTGTTGAATTATAGAGTAGATTAAGGTTTCCCAACTCTTCGCGCCAAACACAGCATAAAATTGTTCATTTATCCTCAAAAAA
TTTTTTGAGGATAAATGAACAATTTTATGCTGTGTTTGGCGCGAAGAGTTGGGAAACCTTAATCTACTCTATAATTCAACAAATACTTTCACTCATCCTT[T/C]
CATTCTTTCATTCATCACTCAATAGATCAGATTCATCCTGTGAAAACCGAACGGTCCAGATCGATCCCCGCCTCCCATCTCTGTCAAACGCGTAATCCCC
| 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 | 68.20% | 3.00% | 9.52% | 19.30% | NA |
| All Indica | 2759 | 69.60% | 4.70% | 13.12% | 12.58% | NA |
| All Japonica | 1512 | 74.30% | 0.20% | 4.50% | 21.03% | NA |
| Aus | 269 | 20.10% | 0.00% | 4.09% | 75.84% | NA |
| Indica I | 595 | 45.70% | 13.40% | 40.17% | 0.67% | NA |
| Indica II | 465 | 80.20% | 3.40% | 6.88% | 9.46% | NA |
| Indica III | 913 | 74.90% | 0.00% | 2.96% | 22.12% | NA |
| Indica Intermediate | 786 | 75.10% | 4.50% | 8.14% | 12.34% | NA |
| Temperate Japonica | 767 | 86.70% | 0.00% | 4.82% | 8.47% | NA |
| Tropical Japonica | 504 | 56.30% | 0.00% | 3.97% | 39.68% | NA |
| Japonica Intermediate | 241 | 72.20% | 1.20% | 4.56% | 21.99% | NA |
| VI/Aromatic | 96 | 65.60% | 0.00% | 2.08% | 32.29% | NA |
| Intermediate | 90 | 71.10% | 7.80% | 7.78% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0403131494 | A -> DEL | N | N | silent_mutation | Average:31.946; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| vg0403131494 | A -> G | LOC_Os04g06030.1 | upstream_gene_variant ; 2798.0bp to feature; MODIFIER | silent_mutation | Average:31.946; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| vg0403131494 | A -> G | LOC_Os04g06030-LOC_Os04g06050 | intergenic_region ; MODIFIER | silent_mutation | Average:31.946; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0403131494 | NA | 3.02E-07 | mr1728 | 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 |
| vg0403131494 | NA | 3.86E-08 | mr1860 | 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 |
| vg0403131494 | NA | 1.11E-09 | mr1860_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 |
| vg0403131494 | NA | 9.21E-07 | mr1860_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 |
| vg0403131494 | NA | 3.65E-07 | mr1904_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 |