Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1110370746:

Variant ID: vg1110370746 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 10370746
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATTAAGATAGAAAAAAAATGTTCGTACGATGCAATGGGAATCCCTTAATTTATCATTCTAAATCGTATATTAGGTGCTCGGGAACGCTTTGCTGCGGAC[T/A]
TAGACGGATTTGTGCGGTTTTTATTATTCTTCTCGTTCAATTTCTCTTCCTCTACATTCTACGTCCGGTTGGATTTTGCATGCGATGTATGGCGCGTGTG

Reverse complement sequence

CACACGCGCCATACATCGCATGCAAAATCCAACCGGACGTAGAATGTAGAGGAAGAGAAATTGAACGAGAAGAATAATAAAAACCGCACAAATCCGTCTA[A/T]
GTCCGCAGCAAAGCGTTCCCGAGCACCTAATATACGATTTAGAATGATAAATTAAGGGATTCCCATTGCATCGTACGAACATTTTTTTTCTATCTTAATA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.50% 1.20% 0.00% 1.31% NA
All Indica  2759 98.00% 1.80% 0.00% 0.11% NA
All Japonica  1512 98.90% 0.40% 0.00% 0.66% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 93.90% 6.10% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.10% 0.70% 0.00% 0.22% NA
Indica Intermediate  786 98.70% 1.10% 0.00% 0.13% NA
Temperate Japonica  767 99.20% 0.70% 0.00% 0.13% NA
Tropical Japonica  504 99.80% 0.00% 0.00% 0.20% NA
Japonica Intermediate  241 96.30% 0.40% 0.00% 3.32% NA
VI/Aromatic  96 51.00% 0.00% 0.00% 48.96% NA
Intermediate  90 97.80% 0.00% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1110370746 T -> A LOC_Os11g18366.2 intron_variant ; MODIFIER silent_mutation Average:37.579; most accessible tissue: Callus, score: 85.679 N N N N
vg1110370746 T -> A LOC_Os11g18366.3 intron_variant ; MODIFIER silent_mutation Average:37.579; most accessible tissue: Callus, score: 85.679 N N N N
vg1110370746 T -> A LOC_Os11g18366.4 intron_variant ; MODIFIER silent_mutation Average:37.579; most accessible tissue: Callus, score: 85.679 N N N N
vg1110370746 T -> DEL N N silent_mutation Average:37.579; most accessible tissue: Callus, score: 85.679 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1110370746 2.01E-06 1.90E-06 mr1154 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
vg1110370746 NA 7.28E-06 mr1092_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
vg1110370746 NA 6.39E-06 mr1152_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
vg1110370746 NA 2.92E-06 mr1154_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
vg1110370746 NA 2.37E-06 mr1914_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