| Variant ID: vg0417784069 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 17784069 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 61. )
CATTGCAAGAACTCCAGAGTGGTATCCAACTTTTTGTGCCCCTGCTCGCAACCTGGGTACAACGACGTTCTGTGGTCCTCTAACATCTTGTCCAATTTAT[G/A]
GGCCCCTTTTCACTTTCGTAGTCCTCCTTGGCGTCCTGCAACATCTGACCAAGATCATCTGCAACGTCGTTACCATCAGCATCCCTTTCCTCCTCGCCCG
CGGGCGAGGAGGAAAGGGATGCTGATGGTAACGACGTTGCAGATGATCTTGGTCAGATGTTGCAGGACGCCAAGGAGGACTACGAAAGTGAAAAGGGGCC[C/T]
ATAAATTGGACAAGATGTTAGAGGACCACAGAACGTCGTTGTACCCAGGTTGCGAGCAGGGGCACAAAAAGTTGGATACCACTCTGGAGTTCTTGCAATG
| 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 | 24.10% | 7.90% | 20.99% | 46.95% | NA |
| All Indica | 2759 | 31.40% | 5.90% | 27.62% | 35.09% | NA |
| All Japonica | 1512 | 6.00% | 9.60% | 5.62% | 78.84% | NA |
| Aus | 269 | 57.20% | 4.50% | 37.55% | 0.74% | NA |
| Indica I | 595 | 54.80% | 8.20% | 9.24% | 27.73% | NA |
| Indica II | 465 | 10.80% | 6.50% | 29.89% | 52.90% | NA |
| Indica III | 913 | 24.30% | 5.50% | 39.98% | 30.23% | NA |
| Indica Intermediate | 786 | 34.00% | 4.50% | 25.83% | 35.75% | NA |
| Temperate Japonica | 767 | 2.50% | 8.60% | 2.48% | 86.44% | NA |
| Tropical Japonica | 504 | 11.30% | 13.10% | 9.92% | 65.67% | NA |
| Japonica Intermediate | 241 | 5.80% | 5.40% | 6.64% | 82.16% | NA |
| VI/Aromatic | 96 | 14.60% | 41.70% | 28.12% | 15.62% | NA |
| Intermediate | 90 | 20.00% | 14.40% | 18.89% | 46.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0417784069 | G -> DEL | N | N | silent_mutation | Average:7.494; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0417784069 | G -> A | LOC_Os04g29830.1 | intron_variant ; MODIFIER | silent_mutation | Average:7.494; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0417784069 | 7.67E-06 | NA | mr1319 | 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 |
| vg0417784069 | NA | 6.50E-06 | mr1367 | 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 |
| vg0417784069 | 8.52E-06 | 3.03E-07 | mr1603 | 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 |
| vg0417784069 | 7.72E-06 | NA | mr1789 | 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 |
| vg0417784069 | 4.55E-06 | NA | mr1864 | 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 |
| vg0417784069 | NA | 4.43E-06 | mr1864 | Ind_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 |
| vg0417784069 | NA | 7.59E-08 | mr1904 | Ind_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 |