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Detailed information for vg1003749596:

Variant ID: vg1003749596 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3749596
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATTCACACACACCAAAGCATGAGCTGAATTACAAGAGGCTCTAGTGTACTTTATTGTATATTAGAATAGGGAGAGAGTACGGTAGAAGGAATCGGAGGA[A/G]
TCCTGGAGTTGTCGATAATCTCTTCTTATCTTTTGTATCTTGTTAATTACTCTGCTTTAATAGAAATATCATTTTGAGTAATTAAGATTTGCTTAGTGAG

Reverse complement sequence

CTCACTAAGCAAATCTTAATTACTCAAAATGATATTTCTATTAAAGCAGAGTAATTAACAAGATACAAAAGATAAGAAGAGATTATCGACAACTCCAGGA[T/C]
TCCTCCGATTCCTTCTACCGTACTCTCTCCCTATTCTAATATACAATAAAGTACACTAGAGCCTCTTGTAATTCAGCTCATGCTTTGGTGTGTGTGAATG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 76.20% 6.20% 2.54% 15.15% NA
All Indica  2759 67.50% 3.30% 3.95% 25.26% NA
All Japonica  1512 90.20% 9.80% 0.00% 0.00% NA
Aus  269 97.00% 2.20% 0.37% 0.37% NA
Indica I  595 84.00% 0.00% 1.85% 14.12% NA
Indica II  465 75.30% 1.50% 3.44% 19.78% NA
Indica III  913 44.40% 7.20% 6.02% 42.39% NA
Indica Intermediate  786 77.40% 2.20% 3.44% 17.05% NA
Temperate Japonica  767 95.00% 5.00% 0.00% 0.00% NA
Tropical Japonica  504 89.50% 10.50% 0.00% 0.00% NA
Japonica Intermediate  241 76.30% 23.70% 0.00% 0.00% NA
VI/Aromatic  96 38.50% 39.60% 9.38% 12.50% NA
Intermediate  90 82.20% 10.00% 1.11% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1003749596 A -> G LOC_Os10g07130.1 upstream_gene_variant ; 3447.0bp to feature; MODIFIER silent_mutation Average:10.643; most accessible tissue: Callus, score: 21.12 N N N N
vg1003749596 A -> G LOC_Os10g07150.2 downstream_gene_variant ; 582.0bp to feature; MODIFIER silent_mutation Average:10.643; most accessible tissue: Callus, score: 21.12 N N N N
vg1003749596 A -> G LOC_Os10g07150.1 downstream_gene_variant ; 582.0bp to feature; MODIFIER silent_mutation Average:10.643; most accessible tissue: Callus, score: 21.12 N N N N
vg1003749596 A -> G LOC_Os10g07130-LOC_Os10g07150 intergenic_region ; MODIFIER silent_mutation Average:10.643; most accessible tissue: Callus, score: 21.12 N N N N
vg1003749596 A -> DEL N N silent_mutation Average:10.643; most accessible tissue: Callus, score: 21.12 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003749596 2.89E-06 1.36E-07 mr1358 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
vg1003749596 NA 2.19E-07 mr1585_2 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