| Variant ID: vg0504490188 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 4490188 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GTTTAAAGATTAGAATTCTAAAAGTTTACTTTGTACTAAGCTTGCTATTATGTATTTTTGTATGGACAAAGAGAAGTACTTTTAGCACTTATATTAACTT[T/G]
TGACCATGCACATGTACTTTTTTAGCACTTGTATTTTGCACAAGATTGAGATTTAAAAATTTAGCTGTGCACAAGCAGTGGTACTGTAGTAGTACCGTTA
TAACGGTACTACTACAGTACCACTGCTTGTGCACAGCTAAATTTTTAAATCTCAATCTTGTGCAAAATACAAGTGCTAAAAAAGTACATGTGCATGGTCA[A/C]
AAGTTAATATAAGTGCTAAAAGTACTTCTCTTTGTCCATACAAAAATACATAATAGCAAGCTTAGTACAAAGTAAACTTTTAGAATTCTAATCTTTAAAC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.20% | 9.50% | 3.20% | 53.07% | NA |
| All Indica | 2759 | 6.30% | 1.80% | 3.62% | 88.26% | NA |
| All Japonica | 1512 | 87.30% | 8.90% | 2.65% | 1.19% | NA |
| Aus | 269 | 1.50% | 90.00% | 1.86% | 6.69% | NA |
| Indica I | 595 | 10.30% | 0.20% | 3.36% | 86.22% | NA |
| Indica II | 465 | 7.10% | 1.50% | 3.44% | 87.96% | NA |
| Indica III | 913 | 2.50% | 0.90% | 3.40% | 93.21% | NA |
| Indica Intermediate | 786 | 7.10% | 4.50% | 4.20% | 84.22% | NA |
| Temperate Japonica | 767 | 97.00% | 1.30% | 0.13% | 1.56% | NA |
| Tropical Japonica | 504 | 70.00% | 21.40% | 7.74% | 0.79% | NA |
| Japonica Intermediate | 241 | 92.50% | 6.60% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 74.00% | 12.50% | 1.04% | 12.50% | NA |
| Intermediate | 90 | 54.40% | 12.20% | 5.56% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0504490188 | T -> DEL | N | N | silent_mutation | Average:10.062; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0504490188 | T -> G | LOC_Os05g08230-LOC_Os05g08240 | intergenic_region ; MODIFIER | silent_mutation | Average:10.062; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0504490188 | 2.06E-08 | 2.06E-08 | mr1929 | 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 |
| vg0504490188 | NA | 1.69E-06 | mr1218_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 |
| vg0504490188 | 5.95E-07 | 2.24E-13 | mr1850_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 |