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Detailed information for vg0710453841:

Variant ID: vg0710453841 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 10453841
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTTTCCACGTGTGCAGGCCGTGTGGTGTCTCGTGGAGTCCTTTTGTCGGCCACTCGCCTCAGTTGACACACGGGATCCGCTTCCGTCGACCCGTGGACC[G/A]
TCTCTGTGTACTTGGTCTACTGTGGTCCCTTAGGTTGACTTGTGGGGTCCACATGTCAACGGCGCAGCCTTCTTGTCTTTTCCAGGCTAGCGCTTATATA

Reverse complement sequence

TATATAAGCGCTAGCCTGGAAAAGACAAGAAGGCTGCGCCGTTGACATGTGGACCCCACAAGTCAACCTAAGGGACCACAGTAGACCAAGTACACAGAGA[C/T]
GGTCCACGGGTCGACGGAAGCGGATCCCGTGTGTCAACTGAGGCGAGTGGCCGACAAAAGGACTCCACGAGACACCACACGGCCTGCACACGTGGAAACC

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 52.30% 21.10% 25.14% 1.46% NA
All Indica  2759 32.00% 32.20% 35.56% 0.25% NA
All Japonica  1512 88.80% 1.60% 8.07% 1.59% NA
Aus  269 61.00% 17.80% 20.45% 0.74% NA
Indica I  595 35.00% 26.90% 38.15% 0.00% NA
Indica II  465 18.50% 42.60% 38.92% 0.00% NA
Indica III  913 31.90% 34.80% 32.86% 0.44% NA
Indica Intermediate  786 37.90% 27.00% 34.73% 0.38% NA
Temperate Japonica  767 83.20% 2.70% 14.08% 0.00% NA
Tropical Japonica  504 93.10% 0.20% 2.58% 4.17% NA
Japonica Intermediate  241 97.50% 0.80% 0.41% 1.24% NA
VI/Aromatic  96 38.50% 13.50% 14.58% 33.33% NA
Intermediate  90 53.30% 24.40% 17.78% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0710453841 G -> DEL N N silent_mutation Average:27.342; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 N N N N
vg0710453841 G -> A LOC_Os07g17700.1 downstream_gene_variant ; 1887.0bp to feature; MODIFIER silent_mutation Average:27.342; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 N N N N
vg0710453841 G -> A LOC_Os07g17710.1 downstream_gene_variant ; 4379.0bp to feature; MODIFIER silent_mutation Average:27.342; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 N N N N
vg0710453841 G -> A LOC_Os07g17700-LOC_Os07g17710 intergenic_region ; MODIFIER silent_mutation Average:27.342; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0710453841 NA 2.78E-06 mr1028 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
vg0710453841 NA 7.03E-06 mr1453 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
vg0710453841 NA 2.21E-07 mr1652 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
vg0710453841 4.63E-06 NA mr1599_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