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Detailed information for vg1001638642:

Variant ID: vg1001638642 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 1638642
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGCTTGCTCGGGCAGCTGGAGGAGGAAGAAGACATATATATATAGGGGTGGGACTTTAGTCCCGGTTGGTAATACCAACCGGGACTAAAGATCCCGGGG[G/A]
GGCCTGACAGGCCCTGGCAGCATTTGAACCGGGACTAAAGATCAAATATGCCCGTTACCCTTTTTAACCGGGACTAAAGATCATCTTTAGCCCCGGTTTT

Reverse complement sequence

AAAACCGGGGCTAAAGATGATCTTTAGTCCCGGTTAAAAAGGGTAACGGGCATATTTGATCTTTAGTCCCGGTTCAAATGCTGCCAGGGCCTGTCAGGCC[C/T]
CCCCGGGATCTTTAGTCCCGGTTGGTATTACCAACCGGGACTAAAGTCCCACCCCTATATATATATGTCTTCTTCCTCCTCCAGCTGCCCGAGCAAGCTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.00% 3.90% 6.81% 35.34% NA
All Indica  2759 24.40% 6.50% 11.05% 58.03% NA
All Japonica  1512 97.80% 0.00% 0.20% 2.05% NA
Aus  269 89.20% 0.00% 4.83% 5.95% NA
Indica I  595 9.10% 4.70% 12.44% 73.78% NA
Indica II  465 12.90% 6.70% 9.68% 70.75% NA
Indica III  913 36.00% 7.70% 12.16% 44.14% NA
Indica Intermediate  786 29.40% 6.40% 9.54% 54.71% NA
Temperate Japonica  767 99.20% 0.00% 0.13% 0.65% NA
Tropical Japonica  504 95.20% 0.00% 0.40% 4.37% NA
Japonica Intermediate  241 98.30% 0.00% 0.00% 1.66% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 71.10% 3.30% 1.11% 24.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1001638642 G -> A LOC_Os10g03660.1 upstream_gene_variant ; 2684.0bp to feature; MODIFIER silent_mutation Average:26.314; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg1001638642 G -> A LOC_Os10g03669.1 downstream_gene_variant ; 3693.0bp to feature; MODIFIER silent_mutation Average:26.314; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg1001638642 G -> A LOC_Os10g03669.2 downstream_gene_variant ; 3775.0bp to feature; MODIFIER silent_mutation Average:26.314; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg1001638642 G -> A LOC_Os10g03660-LOC_Os10g03669 intergenic_region ; MODIFIER silent_mutation Average:26.314; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg1001638642 G -> DEL N N silent_mutation Average:26.314; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1001638642 NA 7.59E-06 mr1383 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
vg1001638642 2.74E-06 NA mr1904 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
vg1001638642 4.99E-08 1.04E-06 mr1904 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
vg1001638642 NA 6.53E-06 mr1721_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