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Detailed information for vg0103668341:

Variant ID: vg0103668341 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 3668341
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


TCAAGAACATTTTTTCAGCTTATCTGTTCTGCTAGGGAAAAGAAGCTCCACTATCTTGCACATCAAATCTTATCAATGCATGTACTCAACAAAAAAAAGG[C/A]
AAAAAAGATCCTGAGAATGACATACAGACTTGTCAAAAAAAAGCTCTATGACGGACGAAACAAAAGGACATATCACAACAAACTGAGTGGACATATAAAG

Reverse complement sequence

CTTTATATGTCCACTCAGTTTGTTGTGATATGTCCTTTTGTTTCGTCCGTCATAGAGCTTTTTTTTGACAAGTCTGTATGTCATTCTCAGGATCTTTTTT[G/T]
CCTTTTTTTTGTTGAGTACATGCATTGATAAGATTTGATGTGCAAGATAGTGGAGCTTCTTTTCCCTAGCAGAACAGATAAGCTGAAAAAATGTTCTTGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.90% 9.90% 0.17% 0.06% NA
All Indica  2759 83.60% 16.00% 0.29% 0.11% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 92.20% 7.80% 0.00% 0.00% NA
Indica I  595 51.10% 47.90% 0.67% 0.34% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 94.00% 6.00% 0.00% 0.00% NA
Indica Intermediate  786 88.00% 11.30% 0.51% 0.13% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 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 98.90% 1.10% 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
vg0103668341 C -> A LOC_Os01g07620.1 upstream_gene_variant ; 2295.0bp to feature; MODIFIER silent_mutation Average:47.422; most accessible tissue: Minghui63 flower, score: 72.332 N N N N
vg0103668341 C -> A LOC_Os01g07610.1 downstream_gene_variant ; 4022.0bp to feature; MODIFIER silent_mutation Average:47.422; most accessible tissue: Minghui63 flower, score: 72.332 N N N N
vg0103668341 C -> A LOC_Os01g07630.1 intron_variant ; MODIFIER silent_mutation Average:47.422; most accessible tissue: Minghui63 flower, score: 72.332 N N N N
vg0103668341 C -> DEL N N silent_mutation Average:47.422; most accessible tissue: Minghui63 flower, score: 72.332 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0103668341 3.81E-06 NA mr1107 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
vg0103668341 NA 7.63E-06 mr1676 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
vg0103668341 NA 4.40E-06 mr1389_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
vg0103668341 NA 3.59E-06 mr1389_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