| Variant ID: vg0205394361 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 5394361 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGTGGCACTTGATTGATCATCTCCACGCCGGGTCATTGCTTGTTACTCTTGGAGGTTGCCGCCTCCTAGACGGCTTGTGGAGGAGTTGTCCGGTGACCTC[T/A]
CCGAGAAAATTGTGGAGGAGGCCCGGCGCCGGTTTGTGAGTGGTTTGGAGTTCACCACCTTCGGAGTGAAGAAAGAACTACCCTAGTGATCGAGGCTTGG
CCAAGCCTCGATCACTAGGGTAGTTCTTTCTTCACTCCGAAGGTGGTGAACTCCAAACCACTCACAAACCGGCGCCGGGCCTCCTCCACAATTTTCTCGG[A/T]
GAGGTCACCGGACAACTCCTCCACAAGCCGTCTAGGAGGCGGCAACCTCCAAGAGTAACAAGCAATGACCCGGCGTGGAGATGATCAATCAAGTGCCACA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 87.60% | 0.70% | 8.04% | 3.72% | NA |
| All Indica | 2759 | 79.80% | 1.20% | 13.05% | 5.94% | NA |
| All Japonica | 1512 | 99.60% | 0.00% | 0.07% | 0.33% | NA |
| Aus | 269 | 94.80% | 0.00% | 4.46% | 0.74% | NA |
| Indica I | 595 | 60.70% | 3.90% | 26.72% | 8.74% | NA |
| Indica II | 465 | 83.90% | 0.60% | 9.03% | 6.45% | NA |
| Indica III | 913 | 88.30% | 0.10% | 9.09% | 2.52% | NA |
| Indica Intermediate | 786 | 82.20% | 0.60% | 9.67% | 7.51% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 0.00% | 6.67% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0205394361 | T -> A | LOC_Os02g10270.1 | downstream_gene_variant ; 1703.0bp to feature; MODIFIER | silent_mutation | Average:18.763; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0205394361 | T -> A | LOC_Os02g10280.1 | downstream_gene_variant ; 1882.0bp to feature; MODIFIER | silent_mutation | Average:18.763; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0205394361 | T -> A | LOC_Os02g10270-LOC_Os02g10280 | intergenic_region ; MODIFIER | silent_mutation | Average:18.763; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0205394361 | T -> DEL | N | N | silent_mutation | Average:18.763; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0205394361 | 3.48E-06 | 8.78E-06 | mr1338_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 |
| vg0205394361 | NA | 8.08E-07 | mr1519_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 |
| vg0205394361 | NA | 1.36E-06 | mr1874_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 |