Variant ID: vg1004990336 (JBrowse) | Variation Type: SNP |
Chromosome: chr10 | Position: 4990336 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CGAACAACGGTTTAAACGTTGAACTTTTCTGTGTTTGTTCCAATTTTCCTCGAAATATACTAATTTGAAACTCGGGACATTACAAGTATAGGGCTCCACC[A/G]
ACATGTGTTTAATTCCAAGTCAAAGTATGCAGGTGAGCATGCATTAAATTCTCCATTAATCATGTTATATATAATTAAGAGAATTTCCTAAATTAAAATA
TATTTTAATTTAGGAAATTCTCTTAATTATATATAACATGATTAATGGAGAATTTAATGCATGCTCACCTGCATACTTTGACTTGGAATTAAACACATGT[T/C]
GGTGGAGCCCTATACTTGTAATGTCCCGAGTTTCAAATTAGTATATTTCGAGGAAAATTGGAACAAACACAGAAAAGTTCAACGTTTAAACCGTTGTTCG
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 | 96.50% | 0.80% | 1.82% | 0.93% | NA |
All Indica | 2759 | 95.90% | 0.00% | 2.75% | 1.38% | NA |
All Japonica | 1512 | 97.50% | 2.40% | 0.13% | 0.00% | NA |
Aus | 269 | 95.90% | 0.00% | 1.86% | 2.23% | NA |
Indica I | 595 | 95.80% | 0.00% | 2.69% | 1.51% | NA |
Indica II | 465 | 95.30% | 0.00% | 3.01% | 1.72% | NA |
Indica III | 913 | 95.60% | 0.00% | 2.96% | 1.42% | NA |
Indica Intermediate | 786 | 96.60% | 0.00% | 2.42% | 1.02% | NA |
Temperate Japonica | 767 | 95.00% | 4.70% | 0.26% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
Intermediate | 90 | 97.80% | 0.00% | 2.22% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1004990336 | A -> G | LOC_Os10g09220.1 | upstream_gene_variant ; 3771.0bp to feature; MODIFIER | silent_mutation | Average:30.003; most accessible tissue: Callus, score: 54.125 | N | N | N | N |
vg1004990336 | A -> G | LOC_Os10g09240.1 | downstream_gene_variant ; 4162.0bp to feature; MODIFIER | silent_mutation | Average:30.003; most accessible tissue: Callus, score: 54.125 | N | N | N | N |
vg1004990336 | A -> G | LOC_Os10g09220-LOC_Os10g09240 | intergenic_region ; MODIFIER | silent_mutation | Average:30.003; most accessible tissue: Callus, score: 54.125 | N | N | N | N |
vg1004990336 | A -> DEL | N | N | silent_mutation | Average:30.003; most accessible tissue: Callus, score: 54.125 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1004990336 | 3.54E-06 | 1.16E-07 | mr1300 | 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 |
vg1004990336 | 7.70E-06 | 3.60E-07 | mr1310 | 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 |
vg1004990336 | NA | 7.76E-06 | mr1959 | 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 |