Variant ID: vg1002106147 (JBrowse) | Variation Type: SNP |
Chromosome: chr10 | Position: 2106147 |
Reference Allele: A | Alternative Allele: T |
Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.59, T: 0.41, others allele: 0.00, population size: 103. )
CTCCATTTATCTTGTATGTTTGCATTATGTCAATAATCATTTAATGAGTTAATTATTTGGAACGACATAACGGATTAGCTCATACTAGCCGCCAACCCGG[A/T]
CGTTGCACAAGCTATTACAAGAAATAAAAATATAAAAAAGACCAAATACATTTTATTGCTTAATAATCTAATTGGCATGAGTACAATGGATGTATGAAGA
TCTTCATACATCCATTGTACTCATGCCAATTAGATTATTAAGCAATAAAATGTATTTGGTCTTTTTTATATTTTTATTTCTTGTAATAGCTTGTGCAACG[T/A]
CCGGGTTGGCGGCTAGTATGAGCTAATCCGTTATGTCGTTCCAAATAATTAACTCATTAAATGATTATTGACATAATGCAAACATACAAGATAAATGGAG
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 | 41.00% | 25.40% | 17.58% | 16.00% | NA |
All Indica | 2759 | 28.10% | 15.50% | 29.25% | 27.11% | NA |
All Japonica | 1512 | 60.70% | 38.80% | 0.26% | 0.26% | NA |
Aus | 269 | 38.70% | 59.50% | 1.49% | 0.37% | NA |
Indica I | 595 | 11.40% | 26.90% | 41.01% | 20.67% | NA |
Indica II | 465 | 28.80% | 4.10% | 32.47% | 34.62% | NA |
Indica III | 913 | 38.90% | 14.00% | 18.62% | 28.48% | NA |
Indica Intermediate | 786 | 27.70% | 15.50% | 30.79% | 25.95% | NA |
Temperate Japonica | 767 | 33.90% | 65.60% | 0.26% | 0.26% | NA |
Tropical Japonica | 504 | 92.90% | 6.90% | 0.20% | 0.00% | NA |
Japonica Intermediate | 241 | 78.80% | 19.90% | 0.41% | 0.83% | NA |
VI/Aromatic | 96 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
Intermediate | 90 | 60.00% | 18.90% | 17.78% | 3.33% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1002106147 | A -> T | LOC_Os10g04460.1 | upstream_gene_variant ; 4515.0bp to feature; MODIFIER | silent_mutation | Average:43.807; most accessible tissue: Minghui63 root, score: 56.226 | N | N | N | N |
vg1002106147 | A -> T | LOC_Os10g04470.1 | downstream_gene_variant ; 1609.0bp to feature; MODIFIER | silent_mutation | Average:43.807; most accessible tissue: Minghui63 root, score: 56.226 | N | N | N | N |
vg1002106147 | A -> T | LOC_Os10g04460-LOC_Os10g04470 | intergenic_region ; MODIFIER | silent_mutation | Average:43.807; most accessible tissue: Minghui63 root, score: 56.226 | N | N | N | N |
vg1002106147 | A -> DEL | N | N | silent_mutation | Average:43.807; most accessible tissue: Minghui63 root, score: 56.226 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1002106147 | NA | 1.38E-13 | Grain_length | All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
vg1002106147 | 8.39E-06 | NA | mr1486 | Ind_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 |
vg1002106147 | 4.59E-07 | NA | mr1588 | 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 |
vg1002106147 | 5.00E-06 | 2.07E-06 | mr1588 | Ind_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 |
vg1002106147 | NA | 1.19E-06 | mr1709 | Ind_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 |
vg1002106147 | NA | 5.53E-09 | mr1709_2 | Ind_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 |