| Variant ID: vg0403594374 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 3594374 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, A: 0.12, others allele: 0.00, population size: 57. )
GCGAAACACCCCCAACCTCGTCTAGTCCCTAGGCGAAGATGTCGATGTTTTTCTTGAGCACAGCCAACATGTTGTTCGTTTCTTCTTCACTTAGATCGCC[A/G]
CCTAGGGAAACCACCTTGGTTTGTTCATCCTCATCAACTTGGACCTTGATCACCTTGCCATGCGGAGATGACTTCGGCATGACTCTTGCTTGTTCACCTT
AAGGTGAACAAGCAAGAGTCATGCCGAAGTCATCTCCGCATGGCAAGGTGATCAAGGTCCAAGTTGATGAGGATGAACAAACCAAGGTGGTTTCCCTAGG[T/C]
GGCGATCTAAGTGAAGAAGAAACGAACAACATGTTGGCTGTGCTCAAGAAAAACATCGACATCTTCGCCTAGGGACTAGACGAGGTTGGGGGTGTTTCGC
| 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 | 32.50% | 19.00% | 0.74% | 47.80% | NA |
| All Indica | 2759 | 51.40% | 2.20% | 0.91% | 45.49% | NA |
| All Japonica | 1512 | 4.80% | 52.60% | 0.20% | 42.39% | NA |
| Aus | 269 | 1.90% | 3.30% | 2.23% | 92.57% | NA |
| Indica I | 595 | 96.10% | 0.50% | 0.17% | 3.19% | NA |
| Indica II | 465 | 50.80% | 4.70% | 1.29% | 43.23% | NA |
| Indica III | 913 | 24.90% | 1.00% | 1.10% | 73.06% | NA |
| Indica Intermediate | 786 | 48.70% | 3.40% | 1.02% | 46.82% | NA |
| Temperate Japonica | 767 | 7.80% | 47.20% | 0.26% | 44.72% | NA |
| Tropical Japonica | 504 | 0.60% | 68.80% | 0.20% | 30.36% | NA |
| Japonica Intermediate | 241 | 3.70% | 36.10% | 0.00% | 60.17% | NA |
| VI/Aromatic | 96 | 4.20% | 7.30% | 1.04% | 87.50% | NA |
| Intermediate | 90 | 38.90% | 27.80% | 0.00% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0403594374 | A -> DEL | N | N | silent_mutation | Average:31.101; most accessible tissue: Zhenshan97 flag leaf, score: 71.238 | N | N | N | N |
| vg0403594374 | A -> G | LOC_Os04g06820.1 | intron_variant ; MODIFIER | silent_mutation | Average:31.101; most accessible tissue: Zhenshan97 flag leaf, score: 71.238 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0403594374 | 2.22E-06 | 9.92E-07 | mr1588 | Ind_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 |
| vg0403594374 | NA | 1.27E-06 | mr1727_2 | 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 |