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Detailed information for vg0904231862:

Variant ID: vg0904231862 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 4231862
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATACCACATGCACCGCCTCTACCTACTCTTCTTTCGGGTGGGGACCCACCCTATCTTGACCGGAACTCGACCCGTGCCTTCGCCTGGAAGCTAAGCCACA[G/A]
CTTGTCCTCAAGTGGGGCCCAGCGCCGTCCCTCGCCTGACACGGGGGACAGCCCTGTCATTCCCCCATTAATGGATGAAGACTTGTGGTGGCCGCCTTCC

Reverse complement sequence

GGAAGGCGGCCACCACAAGTCTTCATCCATTAATGGGGGAATGACAGGGCTGTCCCCCGTGTCAGGCGAGGGACGGCGCTGGGCCCCACTTGAGGACAAG[C/T]
TGTGGCTTAGCTTCCAGGCGAAGGCACGGGTCGAGTTCCGGTCAAGATAGGGTGGGTCCCCACCCGAAAGAAGAGTAGGTAGAGGCGGTGCATGTGGTAT

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 85.20% 5.40% 0.47% 8.89% NA
All Indica  2759 85.80% 0.20% 0.80% 13.16% NA
All Japonica  1512 83.90% 15.90% 0.00% 0.20% NA
Aus  269 99.60% 0.00% 0.00% 0.37% NA
Indica I  595 91.30% 0.80% 0.00% 7.90% NA
Indica II  465 92.00% 0.00% 0.65% 7.31% NA
Indica III  913 75.10% 0.00% 1.75% 23.11% NA
Indica Intermediate  786 90.50% 0.10% 0.38% 9.03% NA
Temperate Japonica  767 79.40% 20.50% 0.00% 0.13% NA
Tropical Japonica  504 96.80% 2.80% 0.00% 0.40% NA
Japonica Intermediate  241 71.00% 29.00% 0.00% 0.00% NA
VI/Aromatic  96 50.00% 5.20% 0.00% 44.79% NA
Intermediate  90 83.30% 5.60% 0.00% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0904231862 G -> DEL N N silent_mutation Average:55.675; most accessible tissue: Zhenshan97 flag leaf, score: 87.472 N N N N
vg0904231862 G -> A LOC_Os09g08170.1 upstream_gene_variant ; 1178.0bp to feature; MODIFIER silent_mutation Average:55.675; most accessible tissue: Zhenshan97 flag leaf, score: 87.472 N N N N
vg0904231862 G -> A LOC_Os09g08160.1 downstream_gene_variant ; 2084.0bp to feature; MODIFIER silent_mutation Average:55.675; most accessible tissue: Zhenshan97 flag leaf, score: 87.472 N N N N
vg0904231862 G -> A LOC_Os09g08180.1 downstream_gene_variant ; 4081.0bp to feature; MODIFIER silent_mutation Average:55.675; most accessible tissue: Zhenshan97 flag leaf, score: 87.472 N N N N
vg0904231862 G -> A LOC_Os09g08160-LOC_Os09g08170 intergenic_region ; MODIFIER silent_mutation Average:55.675; most accessible tissue: Zhenshan97 flag leaf, score: 87.472 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0904231862 6.39E-06 NA Plant_height All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0904231862 NA 2.07E-12 Plant_height Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0904231862 NA 2.96E-06 mr1164_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
vg0904231862 NA 2.71E-07 mr1380_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
vg0904231862 5.97E-07 5.97E-07 mr1908_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
vg0904231862 NA 9.57E-07 mr1996_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