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

Detailed information for vg1003521569:

Variant ID: vg1003521569 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3521569
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGACTTGCCGGTCAGACCGGCCACACACCGCCGGTCTGGCCGGCCCTCCACCGGTGGTCTGACCGGCCAACACATGGCAGTCAGACCGGCCCACTCGGAG[G/A]
AAACTGGCAGACTTCCAAACTTTGGCAATTTTTCCTATTTTTATCCTAAGTGCCAAATTTATGTGTAAATAAATTCTACTGCATTATTCCATTTGTACAA

Reverse complement sequence

TTGTACAAATGGAATAATGCAGTAGAATTTATTTACACATAAATTTGGCACTTAGGATAAAAATAGGAAAAATTGCCAAAGTTTGGAAGTCTGCCAGTTT[C/T]
CTCCGAGTGGGCCGGTCTGACTGCCATGTGTTGGCCGGTCAGACCACCGGTGGAGGGCCGGCCAGACCGGCGGTGTGTGGCCGGTCTGACCGGCAAGTCC

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 79.40% 20.40% 0.23% 0.00% NA
All Indica  2759 65.20% 34.40% 0.40% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 61.20% 38.70% 0.17% 0.00% NA
Indica II  465 75.30% 24.30% 0.43% 0.00% NA
Indica III  913 57.40% 42.20% 0.44% 0.00% NA
Indica Intermediate  786 71.50% 28.00% 0.51% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg1003521569 G -> A LOC_Os10g06760.1 downstream_gene_variant ; 2921.0bp to feature; MODIFIER silent_mutation Average:54.199; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg1003521569 G -> A LOC_Os10g06770.1 downstream_gene_variant ; 4222.0bp to feature; MODIFIER silent_mutation Average:54.199; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg1003521569 G -> A LOC_Os10g06760-LOC_Os10g06770 intergenic_region ; MODIFIER silent_mutation Average:54.199; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003521569 6.23E-12 NA mr1538 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
vg1003521569 2.55E-12 1.00E-13 mr1538 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
vg1003521569 5.43E-18 1.02E-21 mr1547 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
vg1003521569 1.33E-15 1.64E-20 mr1547 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
vg1003521569 2.40E-56 5.27E-61 mr1709 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
vg1003521569 5.21E-51 2.83E-74 mr1709 Ind_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
vg1003521569 NA 4.17E-07 mr1251_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
vg1003521569 NA 6.24E-06 mr1291_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
vg1003521569 NA 5.07E-07 mr1435_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
vg1003521569 1.19E-11 NA mr1538_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
vg1003521569 3.57E-14 1.69E-18 mr1538_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
vg1003521569 7.52E-19 7.42E-24 mr1547_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
vg1003521569 4.57E-19 4.00E-26 mr1547_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
vg1003521569 7.50E-75 1.87E-98 mr1709_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
vg1003521569 1.51E-58 1.50E-103 mr1709_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