Variant ID: vg1120155107 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 20155107 |
Reference Allele: C | Alternative Allele: G,A |
Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTATTTGCAAGAGAGAAAAATAAATATATACTATTCTCCCGGAGAAAATATACGTATGTTTATATGCATGTACAGGAGACTATTATTTGCAAAAAAAAAA[C/G,A]
ATGAATATGTACGTACATAAAAAAAATATTAACCATGTCCTTCTAACCCTTAAATTAGAAAGTTTATACATGATCAGTCTACCCTCTGCTGTGGCTCCTT
AAGGAGCCACAGCAGAGGGTAGACTGATCATGTATAAACTTTCTAATTTAAGGGTTAGAAGGACATGGTTAATATTTTTTTTATGTACGTACATATTCAT[G/C,T]
TTTTTTTTTTGCAAATAATAGTCTCCTGTACATGCATATAAACATACGTATATTTTCTCCGGGAGAATAGTATATATTTATTTTTCTCTCTTGCAAATAC
Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 96.70% | 2.00% | 1.31% | 0.00% | G: 0.02% |
All Indica | 2759 | 99.40% | 0.20% | 0.40% | 0.00% | G: 0.04% |
All Japonica | 1512 | 91.50% | 5.60% | 2.84% | 0.00% | NA |
Aus | 269 | 98.10% | 0.00% | 1.86% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.60% | 0.20% | 0.00% | 0.00% | G: 0.22% |
Indica III | 913 | 99.50% | 0.20% | 0.33% | 0.00% | NA |
Indica Intermediate | 786 | 98.70% | 0.30% | 1.02% | 0.00% | NA |
Temperate Japonica | 767 | 96.90% | 1.20% | 1.96% | 0.00% | NA |
Tropical Japonica | 504 | 80.60% | 14.70% | 4.76% | 0.00% | NA |
Japonica Intermediate | 241 | 97.50% | 0.80% | 1.66% | 0.00% | NA |
VI/Aromatic | 96 | 95.80% | 1.00% | 3.12% | 0.00% | NA |
Intermediate | 90 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1120155107 | C -> A | LOC_Os11g34390.1 | upstream_gene_variant ; 1085.0bp to feature; MODIFIER | silent_mutation | Average:48.949; most accessible tissue: Minghui63 root, score: 68.289 | N | N | N | N |
vg1120155107 | C -> A | LOC_Os11g34410.1 | upstream_gene_variant ; 3400.0bp to feature; MODIFIER | silent_mutation | Average:48.949; most accessible tissue: Minghui63 root, score: 68.289 | N | N | N | N |
vg1120155107 | C -> A | LOC_Os11g34400.1 | downstream_gene_variant ; 2083.0bp to feature; MODIFIER | silent_mutation | Average:48.949; most accessible tissue: Minghui63 root, score: 68.289 | N | N | N | N |
vg1120155107 | C -> A | LOC_Os11g34390-LOC_Os11g34400 | intergenic_region ; MODIFIER | silent_mutation | Average:48.949; most accessible tissue: Minghui63 root, score: 68.289 | N | N | N | N |
vg1120155107 | C -> G | LOC_Os11g34390.1 | upstream_gene_variant ; 1085.0bp to feature; MODIFIER | silent_mutation | Average:48.949; most accessible tissue: Minghui63 root, score: 68.289 | N | N | N | N |
vg1120155107 | C -> G | LOC_Os11g34410.1 | upstream_gene_variant ; 3400.0bp to feature; MODIFIER | silent_mutation | Average:48.949; most accessible tissue: Minghui63 root, score: 68.289 | N | N | N | N |
vg1120155107 | C -> G | LOC_Os11g34400.1 | downstream_gene_variant ; 2083.0bp to feature; MODIFIER | silent_mutation | Average:48.949; most accessible tissue: Minghui63 root, score: 68.289 | N | N | N | N |
vg1120155107 | C -> G | LOC_Os11g34390-LOC_Os11g34400 | intergenic_region ; MODIFIER | silent_mutation | Average:48.949; most accessible tissue: Minghui63 root, score: 68.289 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1120155107 | 1.36E-07 | NA | mr1301_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 |