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Detailed information for vg0514921243:

Variant ID: vg0514921243 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 14921243
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTAATTATACAAAACCGGTCATCCGAGATCCTTCGGCGGTTTTGATCCCAGTTTTGTTCTACGTGACAGCTAAGTCAGCGTGGGACCCATGTGGGCCCCA[C/T]
GTGTCAGCCAACCACTCTCTCTCCCCTTTTCTCTCCCATCTCTCTCACTTCTCTCCTCTCGAGCAAGCCGGGGCGGGTGGGGAGGAGGTCGCAAGGACGG

Reverse complement sequence

CCGTCCTTGCGACCTCCTCCCCACCCGCCCCGGCTTGCTCGAGAGGAGAGAAGTGAGAGAGATGGGAGAGAAAAGGGGAGAGAGAGTGGTTGGCTGACAC[G/A]
TGGGGCCCACATGGGTCCCACGCTGACTTAGCTGTCACGTAGAACAAAACTGGGATCAAAACCGCCGAAGGATCTCGGATGACCGGTTTTGTATAATTAA

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 96.40% 2.40% 1.14% 0.00% NA
All Indica  2759 94.00% 4.10% 1.92% 0.00% NA
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 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 74.80% 16.30% 8.82% 0.00% NA
Indica III  913 99.30% 0.40% 0.22% 0.00% NA
Indica Intermediate  786 94.80% 3.90% 1.27% 0.00% NA
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 95.60% 3.30% 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
vg0514921243 C -> T LOC_Os05g25660.1 upstream_gene_variant ; 149.0bp to feature; MODIFIER silent_mutation Average:67.28; most accessible tissue: Callus, score: 95.649 N N N N
vg0514921243 C -> T LOC_Os05g25650-LOC_Os05g25660 intergenic_region ; MODIFIER silent_mutation Average:67.28; most accessible tissue: Callus, score: 95.649 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0514921243 NA 9.73E-09 mr1045 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
vg0514921243 NA 3.30E-06 mr1045 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
vg0514921243 NA 6.84E-06 mr1749 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
vg0514921243 NA 7.26E-06 mr1790 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
vg0514921243 NA 5.64E-06 mr1941 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
vg0514921243 NA 6.14E-07 mr1336_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
vg0514921243 NA 2.44E-06 mr1425_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
vg0514921243 NA 3.42E-06 mr1908_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
vg0514921243 NA 5.11E-06 mr1977_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