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Detailed information for vg0320074422:

Variant ID: vg0320074422 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 20074422
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


ATCATTTACCTCCAGTAAAATCTACACTAATTAATTTGGTCCACACATTAAGTTATGAAGCTACAAAGTTAGGGGAGAGAAAATAATCTAAAAATTCGTC[T/G]
AAAACCGTGTTCACCCAGAATCTTACCCACCTCTCTCTTCCACCTAGAGCACTTCGTCCTTGGCCCACTTGGCAGCCTCTCCAGCTCGCCCTTTCTCTGT

Reverse complement sequence

ACAGAGAAAGGGCGAGCTGGAGAGGCTGCCAAGTGGGCCAAGGACGAAGTGCTCTAGGTGGAAGAGAGAGGTGGGTAAGATTCTGGGTGAACACGGTTTT[A/C]
GACGAATTTTTAGATTATTTTCTCTCCCCTAACTTTGTAGCTTCATAACTTAATGTGTGGACCAAATTAATTAGTGTAGATTTTACTGGAGGTAAATGAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.40% 3.60% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 89.10% 10.90% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 70.40% 29.60% 0.00% 0.00% NA
Japonica Intermediate  241 93.40% 6.60% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0320074422 T -> G LOC_Os03g36170.1 downstream_gene_variant ; 4394.0bp to feature; MODIFIER silent_mutation Average:47.608; most accessible tissue: Zhenshan97 flag leaf, score: 69.147 N N N N
vg0320074422 T -> G LOC_Os03g36180.1 downstream_gene_variant ; 967.0bp to feature; MODIFIER silent_mutation Average:47.608; most accessible tissue: Zhenshan97 flag leaf, score: 69.147 N N N N
vg0320074422 T -> G LOC_Os03g36180-LOC_Os03g36200 intergenic_region ; MODIFIER silent_mutation Average:47.608; most accessible tissue: Zhenshan97 flag leaf, score: 69.147 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0320074422 NA 5.77E-07 mr1136 Jap_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
vg0320074422 NA 1.06E-07 mr1830 Jap_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
vg0320074422 8.15E-06 1.32E-10 mr1136_2 Jap_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