| Variant ID: vg0809154270 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 9154270 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GCCCCCAGCCGTGAAGTTGGAAAAATCCATTTCCGATTACACAGCTTGGTTAATACGCACGGCGAGAACTCTTACACGACCAGATCTTACATGGTCTTTC[A/G]
TCTCTGAAGGATCCGACAAGGCCTTATCAGCTCTGGGCGTCCCCAGCTGAAGTTCCCTTACGTTCCTCGGAGGCCTTGTCAAGATGACGTAAAGGGACAT
ATGTCCCTTTACGTCATCTTGACAAGGCCTCCGAGGAACGTAAGGGAACTTCAGCTGGGGACGCCCAGAGCTGATAAGGCCTTGTCGGATCCTTCAGAGA[T/C]
GAAAGACCATGTAAGATCTGGTCGTGTAAGAGTTCTCGCCGTGCGTATTAACCAAGCTGTGTAATCGGAAATGGATTTTTCCAACTTCACGGCTGGGGGC
| 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 | 41.00% | 4.10% | 4.10% | 50.72% | NA |
| All Indica | 2759 | 38.30% | 1.20% | 5.11% | 55.42% | NA |
| All Japonica | 1512 | 37.90% | 6.40% | 2.78% | 52.91% | NA |
| Aus | 269 | 96.70% | 0.00% | 0.37% | 2.97% | NA |
| Indica I | 595 | 39.50% | 0.80% | 3.70% | 55.97% | NA |
| Indica II | 465 | 39.40% | 0.90% | 8.60% | 51.18% | NA |
| Indica III | 913 | 35.40% | 1.50% | 3.40% | 59.69% | NA |
| Indica Intermediate | 786 | 40.10% | 1.30% | 6.11% | 52.54% | NA |
| Temperate Japonica | 767 | 61.90% | 9.00% | 1.43% | 27.64% | NA |
| Tropical Japonica | 504 | 6.20% | 1.80% | 5.36% | 86.71% | NA |
| Japonica Intermediate | 241 | 27.80% | 7.90% | 1.66% | 62.66% | NA |
| VI/Aromatic | 96 | 11.50% | 66.70% | 7.29% | 14.58% | NA |
| Intermediate | 90 | 43.30% | 2.20% | 3.33% | 51.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0809154270 | A -> G | LOC_Os08g15110.1 | downstream_gene_variant ; 523.0bp to feature; MODIFIER | silent_mutation | Average:46.955; most accessible tissue: Minghui63 flag leaf, score: 76.453 | N | N | N | N |
| vg0809154270 | A -> G | LOC_Os08g15120.1 | downstream_gene_variant ; 2027.0bp to feature; MODIFIER | silent_mutation | Average:46.955; most accessible tissue: Minghui63 flag leaf, score: 76.453 | N | N | N | N |
| vg0809154270 | A -> G | LOC_Os08g15100.1 | intron_variant ; MODIFIER | silent_mutation | Average:46.955; most accessible tissue: Minghui63 flag leaf, score: 76.453 | N | N | N | N |
| vg0809154270 | A -> DEL | N | N | silent_mutation | Average:46.955; most accessible tissue: Minghui63 flag leaf, score: 76.453 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0809154270 | 3.83E-07 | 3.83E-07 | mr1542 | Jap_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 |
| vg0809154270 | NA | 5.18E-06 | mr1913 | 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 |
| vg0809154270 | NA | 1.32E-06 | mr1062_2 | 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 |