| Variant ID: vg1208597833 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 8597833 |
| Reference Allele: A | Alternative Allele: G,T |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.91, G: 0.09, others allele: 0.00, population size: 76. )
TTCCCTATCATGAGCTGCTTTCTCCTGCTCCACGCTTACTACATCCATGGCGCTAAGCATATACACAGCATGCGTCAGAGTGGCGCTACCTTCGCCTTCA[A/G,T]
GACAGTTGTAAGTTCCATAGTCTTGACCATGAGGCTTGTGTGGATGATACTGGAAAGCTGATGACTCTAACTCCTCATCAAAGCGATGACGTAGCTCTCC
GGAGAGCTACGTCATCGCTTTGATGAGGAGTTAGAGTCATCAGCTTTCCAGTATCATCCACACAAGCCTCATGGTCAAGACTATGGAACTTACAACTGTC[T/C,A]
TGAAGGCGAAGGTAGCGCCACTCTGACGCATGCTGTGTATATGCTTAGCGCCATGGATGTAGTAAGCGTGGAGCAGGAGAAAGCAGCTCATGATAGGGAA
| 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 | 42.90% | 2.30% | 34.07% | 20.76% | T: 0.04% |
| All Indica | 2759 | 42.20% | 3.10% | 48.39% | 6.23% | T: 0.07% |
| All Japonica | 1512 | 45.30% | 0.20% | 3.84% | 50.66% | NA |
| Aus | 269 | 33.10% | 5.20% | 58.74% | 2.97% | NA |
| Indica I | 595 | 69.20% | 1.80% | 25.88% | 3.03% | NA |
| Indica II | 465 | 41.10% | 1.30% | 45.81% | 11.83% | NA |
| Indica III | 913 | 21.70% | 4.60% | 67.47% | 6.13% | T: 0.11% |
| Indica Intermediate | 786 | 46.20% | 3.40% | 44.78% | 5.47% | T: 0.13% |
| Temperate Japonica | 767 | 67.80% | 0.00% | 1.96% | 30.25% | NA |
| Tropical Japonica | 504 | 16.50% | 0.40% | 6.15% | 76.98% | NA |
| Japonica Intermediate | 241 | 34.00% | 0.40% | 4.98% | 60.58% | NA |
| VI/Aromatic | 96 | 43.80% | 3.10% | 36.46% | 16.67% | NA |
| Intermediate | 90 | 51.10% | 1.10% | 26.67% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1208597833 | A -> DEL | N | N | silent_mutation | Average:19.824; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg1208597833 | A -> G | LOC_Os12g15060.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:19.824; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg1208597833 | A -> G | LOC_Os12g15050.1 | downstream_gene_variant ; 4325.0bp to feature; MODIFIER | silent_mutation | Average:19.824; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg1208597833 | A -> T | LOC_Os12g15060.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:19.824; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg1208597833 | A -> T | LOC_Os12g15050.1 | downstream_gene_variant ; 4325.0bp to feature; MODIFIER | silent_mutation | Average:19.824; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1208597833 | NA | 9.57E-06 | mr1448 | 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 |
| vg1208597833 | NA | 9.14E-10 | mr1188_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 |
| vg1208597833 | 3.36E-06 | NA | mr1538_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 |