Variant ID: vg0402345102 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 2345102 |
Reference Allele: A | Alternative Allele: T,C |
Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGGATACAATGTACCGATGATAAGCACCTTCCCTTTTTGTTTACGGCAGTGCCTTGTATGCGCGTAATAAGGGAGAAATGTGTAATACAGACAAGTTCTA[A/T,C]
GAGGATTCTTTTGGAAGATGCGGATATATGATCATGTGTATAATTGTTTACTGACAAAGGAGACCTAGGGTCTCGTGTCAGAGGAACTATGTTCTAACCT
AGGTTAGAACATAGTTCCTCTGACACGAGACCCTAGGTCTCCTTTGTCAGTAAACAATTATACACATGATCATATATCCGCATCTTCCAAAAGAATCCTC[T/A,G]
TAGAACTTGTCTGTATTACACATTTCTCCCTTATTACGCGCATACAAGGCACTGCCGTAAACAAAAAGGGAAGGTGCTTATCATCGGTACATTGTATCCT
Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 81.40% | 7.90% | 5.50% | 3.83% | C: 1.35% |
All Indica | 2759 | 78.70% | 12.60% | 7.21% | 1.27% | C: 0.18% |
All Japonica | 1512 | 88.70% | 0.20% | 2.38% | 4.83% | C: 3.90% |
Aus | 269 | 75.10% | 4.10% | 7.43% | 13.38% | NA |
Indica I | 595 | 95.10% | 1.70% | 1.34% | 1.85% | NA |
Indica II | 465 | 80.40% | 10.50% | 8.60% | 0.22% | C: 0.22% |
Indica III | 913 | 64.10% | 23.50% | 9.75% | 2.19% | C: 0.44% |
Indica Intermediate | 786 | 82.20% | 9.50% | 7.89% | 0.38% | NA |
Temperate Japonica | 767 | 94.50% | 0.10% | 2.09% | 1.96% | C: 1.30% |
Tropical Japonica | 504 | 82.90% | 0.20% | 1.98% | 6.15% | C: 8.73% |
Japonica Intermediate | 241 | 82.20% | 0.40% | 4.15% | 11.20% | C: 2.07% |
VI/Aromatic | 96 | 59.40% | 4.20% | 2.08% | 34.38% | NA |
Intermediate | 90 | 84.40% | 7.80% | 3.33% | 4.44% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0402345102 | A -> C | LOC_Os04g04880.1 | upstream_gene_variant ; 4157.0bp to feature; MODIFIER | silent_mutation | Average:17.378; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |
vg0402345102 | A -> C | LOC_Os04g04860.1 | downstream_gene_variant ; 558.0bp to feature; MODIFIER | silent_mutation | Average:17.378; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |
vg0402345102 | A -> C | LOC_Os04g04870.1 | downstream_gene_variant ; 2418.0bp to feature; MODIFIER | silent_mutation | Average:17.378; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |
vg0402345102 | A -> C | LOC_Os04g04860-LOC_Os04g04870 | intergenic_region ; MODIFIER | silent_mutation | Average:17.378; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |
vg0402345102 | A -> DEL | N | N | silent_mutation | Average:17.378; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |
vg0402345102 | A -> T | LOC_Os04g04880.1 | upstream_gene_variant ; 4157.0bp to feature; MODIFIER | silent_mutation | Average:17.378; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |
vg0402345102 | A -> T | LOC_Os04g04860.1 | downstream_gene_variant ; 558.0bp to feature; MODIFIER | silent_mutation | Average:17.378; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |
vg0402345102 | A -> T | LOC_Os04g04870.1 | downstream_gene_variant ; 2418.0bp to feature; MODIFIER | silent_mutation | Average:17.378; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |
vg0402345102 | A -> T | LOC_Os04g04860-LOC_Os04g04870 | intergenic_region ; MODIFIER | silent_mutation | Average:17.378; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0402345102 | 1.20E-07 | NA | mr1022_2 | 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 |