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Detailed information for vg0903405138:

Variant ID: vg0903405138 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 3405138
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


ATTGTTTGCTTCACCCTGTTTCAGGCTAAATATGGACAGTGGGAAGAAACTGTAAGATGCTAATTGCATACTCCTAATTACTAATGCATCTTAGAAGATG[C/T]
GTAGAATGTTAGAAAAGTAGAGAAGTATCTCTTGTTAGGTTATATGAGTCAAATTCTGTACAAAGATGCCCAGCTCAGATGCACTGCACTCTAATGAAAA

Reverse complement sequence

TTTTCATTAGAGTGCAGTGCATCTGAGCTGGGCATCTTTGTACAGAATTTGACTCATATAACCTAACAAGAGATACTTCTCTACTTTTCTAACATTCTAC[G/A]
CATCTTCTAAGATGCATTAGTAATTAGGAGTATGCAATTAGCATCTTACAGTTTCTTCCCACTGTCCATATTTAGCCTGAAACAGGGTGAAGCAAACAAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.60% 45.40% 0.00% 0.00% NA
All Indica  2759 89.90% 10.10% 0.00% 0.00% NA
All Japonica  1512 0.80% 99.20% 0.00% 0.00% NA
Aus  269 17.80% 82.20% 0.00% 0.00% NA
Indica I  595 94.60% 5.40% 0.00% 0.00% NA
Indica II  465 84.90% 15.10% 0.00% 0.00% NA
Indica III  913 93.40% 6.60% 0.00% 0.00% NA
Indica Intermediate  786 85.00% 15.00% 0.00% 0.00% NA
Temperate Japonica  767 0.70% 99.30% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 40.00% 60.00% 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
vg0903405138 C -> T LOC_Os09g07010.1 upstream_gene_variant ; 2029.0bp to feature; MODIFIER silent_mutation Average:58.339; most accessible tissue: Zhenshan97 root, score: 79.71 N N N N
vg0903405138 C -> T LOC_Os09g07030.1 downstream_gene_variant ; 3742.0bp to feature; MODIFIER silent_mutation Average:58.339; most accessible tissue: Zhenshan97 root, score: 79.71 N N N N
vg0903405138 C -> T LOC_Os09g07020.1 intron_variant ; MODIFIER silent_mutation Average:58.339; most accessible tissue: Zhenshan97 root, score: 79.71 N N N N
vg0903405138 C -> T LOC_Os09g07020.2 intron_variant ; MODIFIER silent_mutation Average:58.339; most accessible tissue: Zhenshan97 root, score: 79.71 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0903405138 NA 4.41E-17 mr1913 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
vg0903405138 NA 1.40E-38 mr1208_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
vg0903405138 NA 2.59E-07 mr1446_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
vg0903405138 NA 1.29E-08 mr1660_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