| Variant ID: vg0520654501 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 20654501 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCCGACAGCTACACGCGTGGCGGCGGCTTCACGCGCCGGATCCGACGGCTACGGCGGTGGTGGCGGCTTCCGGTGATGTTTTATTTTTTTTCCTCTTTCA[C/T]
TTGATTGTCTTATTGGATTTTGTATCTATGTTTGTGATGAATTTTCGCTGAATCACTCGTGCATTTGGTTGTTGATCTGGACTCTAGATGATTTTCTTTT
AAAAGAAAATCATCTAGAGTCCAGATCAACAACCAAATGCACGAGTGATTCAGCGAAAATTCATCACAAACATAGATACAAAATCCAATAAGACAATCAA[G/A]
TGAAAGAGGAAAAAAAATAAAACATCACCGGAAGCCGCCACCACCGCCGTAGCCGTCGGATCCGGCGCGTGAAGCCGCCGCCACGCGTGTAGCTGTCGGG
| 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 | 56.40% | 40.70% | 2.37% | 0.55% | NA |
| All Indica | 2759 | 91.00% | 4.20% | 3.88% | 0.94% | NA |
| All Japonica | 1512 | 2.20% | 97.80% | 0.07% | 0.00% | NA |
| Aus | 269 | 26.40% | 72.90% | 0.74% | 0.00% | NA |
| Indica I | 595 | 91.60% | 2.40% | 5.71% | 0.34% | NA |
| Indica II | 465 | 86.00% | 4.70% | 5.16% | 4.09% | NA |
| Indica III | 913 | 93.50% | 4.30% | 2.19% | 0.00% | NA |
| Indica Intermediate | 786 | 90.60% | 5.10% | 3.69% | 0.64% | NA |
| Temperate Japonica | 767 | 3.70% | 96.20% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 0.60% | 99.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 52.20% | 45.60% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0520654501 | C -> T | LOC_Os05g34800.1 | upstream_gene_variant ; 3971.0bp to feature; MODIFIER | silent_mutation | Average:59.848; most accessible tissue: Zhenshan97 root, score: 75.661 | N | N | N | N |
| vg0520654501 | C -> T | LOC_Os05g34810.1 | downstream_gene_variant ; 2645.0bp to feature; MODIFIER | silent_mutation | Average:59.848; most accessible tissue: Zhenshan97 root, score: 75.661 | N | N | N | N |
| vg0520654501 | C -> T | LOC_Os05g34810-LOC_Os05g34820 | intergenic_region ; MODIFIER | silent_mutation | Average:59.848; most accessible tissue: Zhenshan97 root, score: 75.661 | N | N | N | N |
| vg0520654501 | C -> DEL | N | N | silent_mutation | Average:59.848; most accessible tissue: Zhenshan97 root, score: 75.661 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0520654501 | NA | 5.92E-06 | mr1184_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 |
| vg0520654501 | 2.31E-06 | 2.31E-06 | mr1286_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 |
| vg0520654501 | NA | 4.62E-08 | mr1690_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 |