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Detailed information for vg1020537939:

Variant ID: vg1020537939 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 20537939
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCAATCAACAAAGCCGAAAACAGCATACCTTAAGGTTCCACTGAAAAAGAACATTCCAAACCATACCCAAAACCCGAAAACCACTCCAGCCATTACACAG[A/T]
AGGATAGATACTGGTCCTCGCATTTTCTACAAAATCTCTCATCCGATGCAAGTGAAGAACTTGTGCATGAAATGTTCAATGGAAAGCCACATAGACCATA

Reverse complement sequence

TATGGTCTATGTGGCTTTCCATTGAACATTTCATGCACAAGTTCTTCACTTGCATCGGATGAGAGATTTTGTAGAAAATGCGAGGACCAGTATCTATCCT[T/A]
CTGTGTAATGGCTGGAGTGGTTTTCGGGTTTTGGGTATGGTTTGGAATGTTCTTTTTCAGTGGAACCTTAAGGTATGCTGTTTTCGGCTTTGTTGATTGC

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 81.50% 18.00% 0.51% 0.00% NA
All Indica  2759 98.90% 0.90% 0.11% 0.00% NA
All Japonica  1512 52.60% 46.10% 1.26% 0.00% NA
Aus  269 57.60% 42.00% 0.37% 0.00% NA
Indica I  595 97.60% 2.00% 0.34% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.10% 1.80% 0.13% 0.00% NA
Temperate Japonica  767 27.50% 70.30% 2.22% 0.00% NA
Tropical Japonica  504 89.70% 9.90% 0.40% 0.00% NA
Japonica Intermediate  241 55.20% 44.80% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 83.30% 15.60% 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
vg1020537939 A -> T LOC_Os10g38450.1 3_prime_UTR_variant ; 242.0bp to feature; MODIFIER silent_mutation Average:47.316; most accessible tissue: Callus, score: 82.798 N N N N
vg1020537939 A -> T LOC_Os10g38440.1 upstream_gene_variant ; 3845.0bp to feature; MODIFIER silent_mutation Average:47.316; most accessible tissue: Callus, score: 82.798 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1020537939 1.03E-06 NA mr1071 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
vg1020537939 NA 5.94E-07 mr1124 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
vg1020537939 4.17E-07 4.15E-07 mr1703 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
vg1020537939 NA 1.17E-11 mr1712 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
vg1020537939 NA 6.60E-06 mr1712 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
vg1020537939 NA 3.05E-08 mr1716 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
vg1020537939 NA 1.59E-07 mr1748 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
vg1020537939 NA 1.71E-07 mr1399_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
vg1020537939 NA 1.84E-11 mr1667_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
vg1020537939 NA 4.46E-06 mr1702_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
vg1020537939 NA 1.33E-08 mr1940_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
vg1020537939 NA 1.21E-06 mr1980_2 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