| Variant ID: vg0623074199 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 23074199 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGGCACTAGCCATCCTCTGCGCATCTCTTTGCCTTGCACTGGTGGACAGCTCTGACGCAAGGGAAGCTCCGCACAACAGTCCTGAAATTTTTACATTTTG[A/G]
TCCTTTTTGAAAACTTATTTTACAAATAGACCCCAAAAAAACTTAAACCGGAAATGGTCCTTTTTGGGACGCCAGAGTGGCTGGCGCCGTACCCCAACAT
ATGTTGGGGTACGGCGCCAGCCACTCTGGCGTCCCAAAAAGGACCATTTCCGGTTTAAGTTTTTTTGGGGTCTATTTGTAAAATAAGTTTTCAAAAAGGA[T/C]
CAAAATGTAAAAATTTCAGGACTGTTGTGCGGAGCTTCCCTTGCGTCAGAGCTGTCCACCAGTGCAAGGCAAAGAGATGCGCAGAGGATGGCTAGTGCCA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 44.80% | 24.10% | 6.81% | 24.29% | NA |
| All Indica | 2759 | 58.30% | 2.80% | 10.76% | 28.20% | NA |
| All Japonica | 1512 | 18.80% | 68.50% | 0.40% | 12.30% | NA |
| Aus | 269 | 31.60% | 1.10% | 4.83% | 62.45% | NA |
| Indica I | 595 | 53.80% | 3.50% | 24.71% | 17.98% | NA |
| Indica II | 465 | 66.90% | 4.50% | 8.60% | 20.00% | NA |
| Indica III | 913 | 55.10% | 1.10% | 2.30% | 41.51% | NA |
| Indica Intermediate | 786 | 60.30% | 3.10% | 11.32% | 25.32% | NA |
| Temperate Japonica | 767 | 12.10% | 68.70% | 0.65% | 18.51% | NA |
| Tropical Japonica | 504 | 28.20% | 67.30% | 0.00% | 4.56% | NA |
| Japonica Intermediate | 241 | 20.70% | 70.10% | 0.41% | 8.71% | NA |
| VI/Aromatic | 96 | 90.60% | 2.10% | 1.04% | 6.25% | NA |
| Intermediate | 90 | 55.60% | 27.80% | 5.56% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0623074199 | A -> G | LOC_Os06g38880.1 | downstream_gene_variant ; 4054.0bp to feature; MODIFIER | silent_mutation | Average:78.573; most accessible tissue: Callus, score: 93.333 | N | N | N | N |
| vg0623074199 | A -> G | LOC_Os06g38890.1 | intron_variant ; MODIFIER | silent_mutation | Average:78.573; most accessible tissue: Callus, score: 93.333 | N | N | N | N |
| vg0623074199 | A -> DEL | N | N | silent_mutation | Average:78.573; most accessible tissue: Callus, score: 93.333 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0623074199 | 1.25E-06 | 1.25E-06 | mr1038 | 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 |
| vg0623074199 | NA | 2.67E-08 | mr1666 | 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 |
| vg0623074199 | NA | 3.80E-06 | mr1704 | 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 |