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Detailed information for vg1123834453:

Variant ID: vg1123834453 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 23834453
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GACATATGCTCGGATGTAATTCCCAAGGAATCGGTCCTTAGAGCGAGAACGGACAGACCGTACCTCCAGTACGTCTTCCGTACCGCGAGTTTTAGAAACT[C/T]
ACTTTATTTTCAAGGCACCAACCCAAGTGTCGGGTTTTCCAAGCATTTTGTAAACTCAAGTTTTACCCAGGTGATCAATTTTAGAGTTTGAGGGGAGTCT

Reverse complement sequence

AGACTCCCCTCAAACTCTAAAATTGATCACCTGGGTAAAACTTGAGTTTACAAAATGCTTGGAAAACCCGACACTTGGGTTGGTGCCTTGAAAATAAAGT[G/A]
AGTTTCTAAAACTCGCGGTACGGAAGACGTACTGGAGGTACGGTCTGTCCGTTCTCGCTCTAAGGACCGATTCCTTGGGAATTACATCCGAGCATATGTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.10% 0.20% 1.18% 5.56% NA
All Indica  2759 90.80% 0.30% 1.34% 7.58% NA
All Japonica  1512 98.60% 0.00% 0.00% 1.39% NA
Aus  269 84.80% 0.00% 6.32% 8.92% NA
Indica I  595 84.50% 0.00% 1.85% 13.61% NA
Indica II  465 92.30% 0.90% 0.43% 6.45% NA
Indica III  913 94.10% 0.20% 1.42% 4.27% NA
Indica Intermediate  786 90.80% 0.30% 1.40% 7.51% NA
Temperate Japonica  767 98.40% 0.00% 0.00% 1.56% NA
Tropical Japonica  504 98.40% 0.00% 0.00% 1.59% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 97.90% 0.00% 0.00% 2.08% NA
Intermediate  90 90.00% 0.00% 2.22% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1123834453 C -> T LOC_Os11g39960-LOC_Os11g39990 intergenic_region ; MODIFIER silent_mutation Average:39.378; most accessible tissue: Callus, score: 77.612 N N N N
vg1123834453 C -> DEL N N silent_mutation Average:39.378; most accessible tissue: Callus, score: 77.612 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1123834453 NA 6.63E-06 mr1113_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
vg1123834453 2.33E-07 1.96E-08 mr1238_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
vg1123834453 8.42E-08 8.74E-09 mr1484_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
vg1123834453 NA 6.46E-07 mr1841_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
vg1123834453 NA 1.68E-07 mr1900_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
vg1123834453 4.45E-06 4.44E-06 mr1945_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