Variant ID: vg1102244084 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 2244084 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTTACTGTTATCACCTACACATACTACGCAAAGTTACAGTTTTATGATGATTTCCTACGGTATAATTACAACAAACTGAAATATGATGCTAATGTTGCAG[C/T]
AAACTAATAGTTTTCTCACTATAATTACAGTTTTTCTAAAATTTACTTTTTTTTTCTCAGTTATTTGTAAGTAATTATTACATTTGAGTTTATAATATTA
TAATATTATAAACTCAAATGTAATAATTACTTACAAATAACTGAGAAAAAAAAAGTAAATTTTAGAAAAACTGTAATTATAGTGAGAAAACTATTAGTTT[G/A]
CTGCAACATTAGCATCATATTTCAGTTTGTTGTAATTATACCGTAGGAAATCATCATAAAACTGTAACTTTGCGTAGTATGTGTAGGTGATAACAGTAAG
Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 98.00% | 1.40% | 0.59% | 0.00% | NA |
All Indica | 2759 | 100.00% | 0.00% | 0.04% | 0.00% | NA |
All Japonica | 1512 | 94.00% | 4.20% | 1.79% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 90.50% | 6.60% | 2.87% | 0.00% | NA |
Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
Japonica Intermediate | 241 | 92.90% | 5.40% | 1.66% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 98.90% | 1.10% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg1102244084 | C -> T | LOC_Os11g05110.1 | upstream_gene_variant ; 585.0bp to feature; MODIFIER | silent_mutation | Average:64.519; most accessible tissue: Minghui63 panicle, score: 84.552 | N | N | N | N |
vg1102244084 | C -> T | LOC_Os11g05110.3 | upstream_gene_variant ; 585.0bp to feature; MODIFIER | silent_mutation | Average:64.519; most accessible tissue: Minghui63 panicle, score: 84.552 | N | N | N | N |
vg1102244084 | C -> T | LOC_Os11g05110.2 | upstream_gene_variant ; 480.0bp to feature; MODIFIER | silent_mutation | Average:64.519; most accessible tissue: Minghui63 panicle, score: 84.552 | N | N | N | N |
vg1102244084 | C -> T | LOC_Os11g05100.1 | downstream_gene_variant ; 4982.0bp to feature; MODIFIER | silent_mutation | Average:64.519; most accessible tissue: Minghui63 panicle, score: 84.552 | N | N | N | N |
vg1102244084 | C -> T | LOC_Os11g05120.1 | downstream_gene_variant ; 961.0bp to feature; MODIFIER | silent_mutation | Average:64.519; most accessible tissue: Minghui63 panicle, score: 84.552 | N | N | N | N |
vg1102244084 | C -> T | LOC_Os11g05130.1 | downstream_gene_variant ; 3622.0bp to feature; MODIFIER | silent_mutation | Average:64.519; most accessible tissue: Minghui63 panicle, score: 84.552 | N | N | N | N |
vg1102244084 | C -> T | LOC_Os11g05130.2 | downstream_gene_variant ; 3622.0bp to feature; MODIFIER | silent_mutation | Average:64.519; most accessible tissue: Minghui63 panicle, score: 84.552 | N | N | N | N |
vg1102244084 | C -> T | LOC_Os11g05110-LOC_Os11g05120 | intergenic_region ; MODIFIER | silent_mutation | Average:64.519; most accessible tissue: Minghui63 panicle, score: 84.552 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1102244084 | 2.24E-06 | 2.24E-06 | mr1172_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 |