| Variant ID: vg0205011592 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 5011592 |
| Reference Allele: T | Alternative Allele: C,G |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ATTAGATCTATTATTTAAGAAAGTAATCCCTTCCTCTGCTGTGAGCCAGAAAAAGAAAAAAAAACGTACGTACGTACGTAAGTGTGGCTTCGTATAACCG[T/C,G]
GGGCCGGAAAAAGAAAAAAAACATAAGAACGTAGTACGCTCTCCTGTCTCTTCCTCTTCCTATTCTTTTATATCTCCATCTTTTTCTCTTCGTAATTCTT
AAGAATTACGAAGAGAAAAAGATGGAGATATAAAAGAATAGGAAGAGGAAGAGACAGGAGAGCGTACTACGTTCTTATGTTTTTTTTCTTTTTCCGGCCC[A/G,C]
CGGTTATACGAAGCCACACTTACGTACGTACGTACGTTTTTTTTTCTTTTTCTGGCTCACAGCAGAGGAAGGGATTACTTTCTTAAATAATAGATCTAAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.40% | 13.80% | 1.27% | 2.50% | NA |
| All Indica | 2759 | 81.30% | 13.60% | 1.63% | 3.44% | NA |
| All Japonica | 1512 | 99.30% | 0.60% | 0.07% | 0.00% | NA |
| Aus | 269 | 23.40% | 68.00% | 3.35% | 5.20% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 69.00% | 19.60% | 4.09% | 7.31% | NA |
| Indica III | 913 | 74.00% | 20.60% | 1.20% | 4.16% | NA |
| Indica Intermediate | 786 | 83.00% | 12.20% | 1.91% | 2.93% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 24.00% | 68.80% | 2.08% | 5.21% | NA |
| Intermediate | 90 | 72.20% | 20.00% | 3.33% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0205011592 | T -> G | LOC_Os02g09730.1 | upstream_gene_variant ; 3245.0bp to feature; MODIFIER | N | Average:55.828; most accessible tissue: Zhenshan97 root, score: 77.417 | N | N | N | N |
| vg0205011592 | T -> G | LOC_Os02g09720-LOC_Os02g09730 | intergenic_region ; MODIFIER | N | Average:55.828; most accessible tissue: Zhenshan97 root, score: 77.417 | N | N | N | N |
| vg0205011592 | T -> DEL | N | N | silent_mutation | Average:55.828; most accessible tissue: Zhenshan97 root, score: 77.417 | N | N | N | N |
| vg0205011592 | T -> C | LOC_Os02g09730.1 | upstream_gene_variant ; 3245.0bp to feature; MODIFIER | silent_mutation | Average:55.828; most accessible tissue: Zhenshan97 root, score: 77.417 | N | N | N | N |
| vg0205011592 | T -> C | LOC_Os02g09720-LOC_Os02g09730 | intergenic_region ; MODIFIER | silent_mutation | Average:55.828; most accessible tissue: Zhenshan97 root, score: 77.417 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0205011592 | NA | 5.05E-08 | mr1403 | 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 |
| vg0205011592 | NA | 7.42E-07 | mr1808 | 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 |
| vg0205011592 | 3.11E-06 | NA | mr1889 | 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 |
| vg0205011592 | NA | 1.09E-07 | mr1612_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 |