| Variant ID: vg0411851800 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 11851800 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TAAGTATTTTACGCTTTATTTACGTTTGGAACTGTATATTACTTGTCGTTTTCTGTACCCTGGCTGGTCCTGGACAGAGATTTAATACGCAAAATAGTCT[A/G]
GAAATTTGGGTTAAATTTCTGGGCGTGACAAAGTGGTATCAGAGCCAACTTGACTGTAGGTTGAGCCAAATGGTCAAACCCTAAGGACAAGTTTTCTGAA
TTCAGAAAACTTGTCCTTAGGGTTTGACCATTTGGCTCAACCTACAGTCAAGTTGGCTCTGATACCACTTTGTCACGCCCAGAAATTTAACCCAAATTTC[T/C]
AGACTATTTTGCGTATTAAATCTCTGTCCAGGACCAGCCAGGGTACAGAAAACGACAAGTAATATACAGTTCCAAACGTAAATAAAGCGTAAAATACTTA
| 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 | 25.90% | 0.40% | 27.59% | 46.09% | NA |
| All Indica | 2759 | 12.00% | 0.50% | 43.28% | 44.26% | NA |
| All Japonica | 1512 | 51.70% | 0.10% | 1.46% | 46.76% | NA |
| Aus | 269 | 5.90% | 1.90% | 20.45% | 71.75% | NA |
| Indica I | 595 | 9.60% | 0.00% | 23.70% | 66.72% | NA |
| Indica II | 465 | 13.80% | 1.50% | 55.48% | 29.25% | NA |
| Indica III | 913 | 13.90% | 0.10% | 50.49% | 35.49% | NA |
| Indica Intermediate | 786 | 10.60% | 0.60% | 42.49% | 46.31% | NA |
| Temperate Japonica | 767 | 85.30% | 0.00% | 0.65% | 14.08% | NA |
| Tropical Japonica | 504 | 5.40% | 0.00% | 2.38% | 92.26% | NA |
| Japonica Intermediate | 241 | 41.90% | 0.40% | 2.07% | 55.60% | NA |
| VI/Aromatic | 96 | 70.80% | 0.00% | 11.46% | 17.71% | NA |
| Intermediate | 90 | 30.00% | 1.10% | 24.44% | 44.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0411851800 | A -> DEL | N | N | silent_mutation | Average:13.097; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0411851800 | A -> G | LOC_Os04g21090.1 | upstream_gene_variant ; 753.0bp to feature; MODIFIER | silent_mutation | Average:13.097; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0411851800 | A -> G | LOC_Os04g21080-LOC_Os04g21090 | intergenic_region ; MODIFIER | silent_mutation | Average:13.097; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0411851800 | NA | 6.18E-06 | mr1482 | 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 |
| vg0411851800 | 3.68E-06 | NA | mr1549 | 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 |
| vg0411851800 | 3.65E-07 | 2.43E-07 | mr1550 | 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 |
| vg0411851800 | 3.50E-06 | 3.50E-06 | mr1716 | 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 |
| vg0411851800 | NA | 4.24E-08 | mr1757 | 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 |
| vg0411851800 | 2.02E-06 | 1.06E-06 | mr1550_2 | 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 |