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Detailed information for vg0202348990:

Variant ID: vg0202348990 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 2348990
Reference Allele: TAlternative Allele: C,TC
Primary Allele: TSecondary Allele: TC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTCAAGACTAGAACCCATGATCCCCCATGGCCCCACCCACTCCCGGCGGGCCTCCTTCCTCTCGATCTCTCTCCCGATCTCTCCGTCCCTTCTTTTTTT[T/C,TC]
CTTCTCCCTCCTCTTATTTTTTCCTTCTATTCTTTTCTTTTTTTTAGAAAAACTAAAAATAAATTGGTGAATTCAAGACTATAACTCTCTCCCGATCTCT

Reverse complement sequence

AGAGATCGGGAGAGAGTTATAGTCTTGAATTCACCAATTTATTTTTAGTTTTTCTAAAAAAAAGAAAAGAATAGAAGGAAAAAATAAGAGGAGGGAGAAG[A/G,GA]
AAAAAAAGAAGGGACGGAGAGATCGGGAGAGAGATCGAGAGGAAGGAGGCCCGCCGGGAGTGGGTGGGGCCATGGGGGATCATGGGTTCTAGTCTTGAAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of TC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.30% 4.10% 0.21% 0.00% C: 0.32%
All Indica  2759 92.00% 7.10% 0.33% 0.00% C: 0.54%
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 87.60% 10.60% 0.84% 0.00% C: 1.01%
Indica II  465 98.90% 0.40% 0.43% 0.00% C: 0.22%
Indica III  913 89.80% 9.50% 0.00% 0.00% C: 0.66%
Indica Intermediate  786 93.90% 5.60% 0.25% 0.00% C: 0.25%
Temperate Japonica  767 100.00% 0.00% 0.00% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0202348990 T -> TC LOC_Os02g04980.1 upstream_gene_variant ; 3136.0bp to feature; MODIFIER silent_mutation Average:42.833; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0202348990 T -> TC LOC_Os02g04970.1 downstream_gene_variant ; 3486.0bp to feature; MODIFIER silent_mutation Average:42.833; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0202348990 T -> TC LOC_Os02g04970-LOC_Os02g04980 intergenic_region ; MODIFIER silent_mutation Average:42.833; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0202348990 T -> C LOC_Os02g04980.1 upstream_gene_variant ; 3137.0bp to feature; MODIFIER silent_mutation Average:42.833; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0202348990 T -> C LOC_Os02g04970.1 downstream_gene_variant ; 3485.0bp to feature; MODIFIER silent_mutation Average:42.833; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0202348990 T -> C LOC_Os02g04970-LOC_Os02g04980 intergenic_region ; MODIFIER silent_mutation Average:42.833; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0202348990 NA 9.36E-06 mr1718 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
vg0202348990 4.10E-08 4.10E-08 mr1276_2 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