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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0721964052:

Variant ID: vg0721964052 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 21964052
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGAAGCACCTTCATAGTTATCACAAGTGCATATTTGTGCTTGGACAATTAATCCGCTCTACGCGTGTAGGATGTGAATAATGTCCCTAACACATGGTCCC[A/G]
ATGATTGTAGCATTGGAGAAACGGACGTCCGAGCAATGCACCTTTACGTATAAGTAAATAATGAATATTTTGGGAGTTCATTAATTATTTTAAACTACAT

Reverse complement sequence

ATGTAGTTTAAAATAATTAATGAACTCCCAAAATATTCATTATTTACTTATACGTAAAGGTGCATTGCTCGGACGTCCGTTTCTCCAATGCTACAATCAT[T/C]
GGGACCATGTGTTAGGGACATTATTCACATCCTACACGCGTAGAGCGGATTAATTGTCCAAGCACAAATATGCACTTGTGATAACTATGAAGGTGCTTCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.10% 39.90% 0.04% 0.00% NA
All Indica  2759 88.50% 11.50% 0.04% 0.00% NA
All Japonica  1512 1.30% 98.70% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 97.50% 2.40% 0.17% 0.00% NA
Indica II  465 82.20% 17.80% 0.00% 0.00% NA
Indica III  913 87.20% 12.80% 0.00% 0.00% NA
Indica Intermediate  786 87.00% 13.00% 0.00% 0.00% NA
Temperate Japonica  767 1.40% 98.60% 0.00% 0.00% NA
Tropical Japonica  504 0.20% 99.80% 0.00% 0.00% NA
Japonica Intermediate  241 3.30% 96.70% 0.00% 0.00% NA
VI/Aromatic  96 67.70% 31.20% 1.04% 0.00% NA
Intermediate  90 48.90% 51.10% 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
vg0721964052 A -> G LOC_Os07g36680-LOC_Os07g36690 intergenic_region ; MODIFIER silent_mutation Average:36.616; most accessible tissue: Zhenshan97 panicle, score: 71.253 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0721964052 NA 7.91E-16 mr1324 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
vg0721964052 NA 4.34E-11 mr1325 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
vg0721964052 NA 1.07E-12 mr1326 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
vg0721964052 NA 7.24E-07 mr1338 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
vg0721964052 NA 3.19E-08 mr1439 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
vg0721964052 NA 2.03E-10 mr1623 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
vg0721964052 NA 1.82E-09 mr1644 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
vg0721964052 NA 2.43E-16 mr1146_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
vg0721964052 NA 1.79E-07 mr1821_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