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Detailed information for vg0403236974:

Variant ID: vg0403236974 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 3236974
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCTATTTATCGTCGTAAACACGGTGAACAAAAACTATGTGCCCAGGTTTCTCTACTTGGACCCATGTCAAAACATGACACGTATAGGATAATTGGCATC[T/C]
AAGATTAATCGTTTAATTTCATAACTGAACTAGTGTTTGAATTAAGATGGGTCGTCTAGAGATTTGGTTTTATAGGAATCTTTTTTTCCATGTAGTCATG

Reverse complement sequence

CATGACTACATGGAAAAAAAGATTCCTATAAAACCAAATCTCTAGACGACCCATCTTAATTCAAACACTAGTTCAGTTATGAAATTAAACGATTAATCTT[A/G]
GATGCCAATTATCCTATACGTGTCATGTTTTGACATGGGTCCAAGTAGAGAAACCTGGGCACATAGTTTTTGTTCACCGTGTTTACGACGATAAATAGGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.10% 2.60% 0.06% 0.23% NA
All Indica  2759 96.00% 3.90% 0.07% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 92.90% 3.00% 0.00% 4.09% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 87.30% 12.50% 0.22% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 94.80% 5.10% 0.13% 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 93.30% 5.60% 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
vg0403236974 T -> C LOC_Os04g06230.1 upstream_gene_variant ; 1539.0bp to feature; MODIFIER silent_mutation Average:19.024; most accessible tissue: Callus, score: 47.152 N N N N
vg0403236974 T -> C LOC_Os04g06244.1 upstream_gene_variant ; 1840.0bp to feature; MODIFIER silent_mutation Average:19.024; most accessible tissue: Callus, score: 47.152 N N N N
vg0403236974 T -> C LOC_Os04g06230-LOC_Os04g06244 intergenic_region ; MODIFIER silent_mutation Average:19.024; most accessible tissue: Callus, score: 47.152 N N N N
vg0403236974 T -> DEL N N silent_mutation Average:19.024; most accessible tissue: Callus, score: 47.152 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0403236974 1.97E-07 2.24E-11 mr1310 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
vg0403236974 NA 8.06E-12 mr1498 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
vg0403236974 NA 5.20E-08 mr1925 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
vg0403236974 NA 7.77E-09 mr1951 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
vg0403236974 NA 1.16E-08 mr1310_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
vg0403236974 NA 1.98E-08 mr1498_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
vg0403236974 NA 6.86E-09 mr1769_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
vg0403236974 NA 1.53E-07 mr1951_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