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Detailed information for vg0207033231:

Variant ID: vg0207033231 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 7033231
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


CAACCAAATAACCCGTGAACATTATAAGAACAACATGAAGACCTGAAAATAGAAGCACAGCAATCAATTGTACAGTGGAATACCATACAAGCTGATATTA[G/C]
CAGCCCTAGCTCCAGGCTGAAGGTACATTAAGTAGTGAGATTTAAAGAGGATTAAGTGTGCTATAATTGGCATGCTGGTTCACCTATCTACAGCAAAGGA

Reverse complement sequence

TCCTTTGCTGTAGATAGGTGAACCAGCATGCCAATTATAGCACACTTAATCCTCTTTAAATCTCACTACTTAATGTACCTTCAGCCTGGAGCTAGGGCTG[C/G]
TAATATCAGCTTGTATGGTATTCCACTGTACAATTGATTGCTGTGCTTCTATTTTCAGGTCTTCATGTTGTTCTTATAATGTTCACGGGTTATTTGGTTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.80% 4.20% 0.00% 0.00% NA
All Indica  2759 96.10% 3.90% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 69.90% 30.10% 0.00% 0.00% NA
Indica I  595 87.40% 12.60% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 96.40% 3.60% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 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% 4.40% 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
vg0207033231 G -> C LOC_Os02g13190.1 upstream_gene_variant ; 4927.0bp to feature; MODIFIER silent_mutation Average:70.289; most accessible tissue: Callus, score: 86.236 N N N N
vg0207033231 G -> C LOC_Os02g13200.1 intron_variant ; MODIFIER silent_mutation Average:70.289; most accessible tissue: Callus, score: 86.236 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0207033231 NA 2.94E-07 mr1053_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
vg0207033231 5.82E-06 1.24E-06 mr1128_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
vg0207033231 NA 5.58E-07 mr1147_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