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Detailed information for vg0721652148:

Variant ID: vg0721652148 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 21652148
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TGATCCTACAAAGGGCATCTTGACGAGTAGTAGTAGTAGTTTGCACACCAAACCGGCCGACTATATGATACTGGAGTAGTAGTTCTTTTCATTTACATAT[C/G]
AAAATGCCGTCTTAAGGCGTGTCATTCCGTCAGTCTTGTAAAGCTGAAAACAAACATTTATTATCCGTTTGTAAACAATTATTTGCTCCTAAAGAAATGT

Reverse complement sequence

ACATTTCTTTAGGAGCAAATAATTGTTTACAAACGGATAATAAATGTTTGTTTTCAGCTTTACAAGACTGACGGAATGACACGCCTTAAGACGGCATTTT[G/C]
ATATGTAAATGAAAAGAACTACTACTCCAGTATCATATAGTCGGCCGGTTTGGTGTGCAAACTACTACTACTACTCGTCAAGATGCCCTTTGTAGGATCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.00% 8.00% 0.00% 0.00% NA
All Indica  2759 86.30% 13.70% 0.00% 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 98.00% 2.00% 0.00% 0.00% NA
Indica II  465 92.30% 7.70% 0.00% 0.00% NA
Indica III  913 78.10% 21.90% 0.00% 0.00% NA
Indica Intermediate  786 83.50% 16.50% 0.00% 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  90 100.00% 0.00% 0.00% 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
vg0721652148 C -> G LOC_Os07g36230.1 upstream_gene_variant ; 1106.0bp to feature; MODIFIER silent_mutation Average:55.798; most accessible tissue: Callus, score: 91.398 N N N N
vg0721652148 C -> G LOC_Os07g36230.3 upstream_gene_variant ; 1574.0bp to feature; MODIFIER silent_mutation Average:55.798; most accessible tissue: Callus, score: 91.398 N N N N
vg0721652148 C -> G LOC_Os07g36230.2 upstream_gene_variant ; 2495.0bp to feature; MODIFIER silent_mutation Average:55.798; most accessible tissue: Callus, score: 91.398 N N N N
vg0721652148 C -> G LOC_Os07g36230.4 upstream_gene_variant ; 2672.0bp to feature; MODIFIER silent_mutation Average:55.798; most accessible tissue: Callus, score: 91.398 N N N N
vg0721652148 C -> G LOC_Os07g36220-LOC_Os07g36230 intergenic_region ; MODIFIER silent_mutation Average:55.798; most accessible tissue: Callus, score: 91.398 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0721652148 3.06E-06 5.63E-07 mr1528_2 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
vg0721652148 3.26E-06 3.40E-08 mr1528_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