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Detailed information for vg0622020773:

Variant ID: vg0622020773 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 22020773
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCTAATATGTTTACGTGACTATATCTTAATCGGGCACTTTTTTTTGTCCCGATTGAGATGACTTCCTAGTGATAGCCCAATAATTCTAGGCATGTTAGA[G/T]
GCCATCACAGATGGAAGGATCTGTACTGTGCAAACAAAAGAAAACACTTATATGTCCATCGTACCTGGAGAGGTGTAATGCTTTTTTTCTCTATTTGATT

Reverse complement sequence

AATCAAATAGAGAAAAAAAGCATTACACCTCTCCAGGTACGATGGACATATAAGTGTTTTCTTTTGTTTGCACAGTACAGATCCTTCCATCTGTGATGGC[C/A]
TCTAACATGCCTAGAATTATTGGGCTATCACTAGGAAGTCATCTCAATCGGGACAAAAAAAAGTGCCCGATTAAGATATAGTCACGTAAACATATTAGAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.50% 3.40% 1.12% 0.00% NA
All Indica  2759 99.00% 1.00% 0.00% 0.00% NA
All Japonica  1512 88.40% 8.30% 3.31% 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 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 2.40% 0.00% 0.00% NA
Temperate Japonica  767 95.80% 0.90% 3.26% 0.00% NA
Tropical Japonica  504 77.20% 20.80% 1.98% 0.00% NA
Japonica Intermediate  241 88.40% 5.40% 6.22% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 8.90% 3.33% 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
vg0622020773 G -> T LOC_Os06g37300.1 downstream_gene_variant ; 67.0bp to feature; MODIFIER silent_mutation Average:61.205; most accessible tissue: Zhenshan97 root, score: 68.908 N N N N
vg0622020773 G -> T LOC_Os06g37300.2 downstream_gene_variant ; 67.0bp to feature; MODIFIER silent_mutation Average:61.205; most accessible tissue: Zhenshan97 root, score: 68.908 N N N N
vg0622020773 G -> T LOC_Os06g37290-LOC_Os06g37300 intergenic_region ; MODIFIER silent_mutation Average:61.205; most accessible tissue: Zhenshan97 root, score: 68.908 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0622020773 NA 2.10E-06 mr1125 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
vg0622020773 4.10E-06 6.20E-12 mr1136 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
vg0622020773 3.22E-07 4.98E-10 mr1188 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
vg0622020773 NA 7.87E-07 mr1448 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
vg0622020773 NA 2.89E-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
vg0622020773 NA 1.49E-07 mr1125_2 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
vg0622020773 1.53E-07 1.15E-12 mr1188_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