| Variant ID: vg1110012570 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 10012570 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GACAGTGGCGCGCCAGGTAGGGGGATTTTGGTGCTTCAGGATTTCGACGAGATGGTTTCAAAAGATGGATTCTCCAGCAACAAGCTACTCGACAGCTTCG[A/G]
ACCAGGGAGATCCAACCCGGCCAGAGTACGTCTCCCAACGAGATTGGAATCATCGTCATCAACTATTCGATCCGGCGAGATCGATCAAGCTCCAAAATAT
ATATTTTGGAGCTTGATCGATCTCGCCGGATCGAATAGTTGATGACGATGATTCCAATCTCGTTGGGAGACGTACTCTGGCCGGGTTGGATCTCCCTGGT[T/C]
CGAAGCTGTCGAGTAGCTTGTTGCTGGAGAATCCATCTTTTGAAACCATCTCGTCGAAATCCTGAAGCACCAAAATCCCCCTACCTGGCGCGCCACTGTC
| 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 | 44.10% | 3.40% | 2.24% | 50.23% | NA |
| All Indica | 2759 | 20.30% | 1.80% | 2.50% | 75.39% | NA |
| All Japonica | 1512 | 93.70% | 2.00% | 2.31% | 1.98% | NA |
| Aus | 269 | 18.20% | 0.70% | 0.37% | 80.67% | NA |
| Indica I | 595 | 38.20% | 6.40% | 2.35% | 53.11% | NA |
| Indica II | 465 | 19.80% | 0.00% | 0.86% | 79.35% | NA |
| Indica III | 913 | 3.20% | 0.40% | 2.08% | 94.30% | NA |
| Indica Intermediate | 786 | 26.80% | 1.10% | 4.07% | 67.94% | NA |
| Temperate Japonica | 767 | 93.20% | 0.70% | 4.17% | 1.96% | NA |
| Tropical Japonica | 504 | 94.00% | 3.00% | 0.40% | 2.58% | NA |
| Japonica Intermediate | 241 | 94.60% | 4.10% | 0.41% | 0.83% | NA |
| VI/Aromatic | 96 | 19.80% | 70.80% | 0.00% | 9.38% | NA |
| Intermediate | 90 | 44.40% | 12.20% | 1.11% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1110012570 | A -> DEL | LOC_Os11g17880.1 | N | frameshift_variant | Average:15.25; most accessible tissue: Callus, score: 33.825 | N | N | N | N |
| vg1110012570 | A -> G | LOC_Os11g17880.1 | missense_variant ; p.Asn13Asp; MODERATE | nonsynonymous_codon | Average:15.25; most accessible tissue: Callus, score: 33.825 | unknown | unknown | TOLERATED | 0.42 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1110012570 | 9.42E-06 | NA | mr1247 | 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 |
| vg1110012570 | 4.48E-06 | 9.53E-06 | mr1240_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 |
| vg1110012570 | 4.93E-06 | NA | mr1449_2 | 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 |