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Detailed information for vg1205351745:

Variant ID: vg1205351745 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 5351745
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


TAGATCCTTGTTTGTTTATGGAAACAACCTAGCAATCTTGCATGGCTTTCTCATGGATACGTAGTCTATCTCTTTTCTCTTTATTGTCCTTCATGATACT[C/T]
CCATGTCACAGATAGTGCTTTTGTGGTTACTAACGGCTTAGTCGAGACTTCACTTCTACTATACGAGTGTGTGACTAGAGGAAACTAGTACTAACAATAA

Reverse complement sequence

TTATTGTTAGTACTAGTTTCCTCTAGTCACACACTCGTATAGTAGAAGTGAAGTCTCGACTAAGCCGTTAGTAACCACAAAAGCACTATCTGTGACATGG[G/A]
AGTATCATGAAGGACAATAAAGAGAAAAGAGATAGACTACGTATCCATGAGAAAGCCATGCAAGATTGCTAGGTTGTTTCCATAAACAAACAAGGATCTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.70% 1.20% 0.08% 0.00% NA
All Indica  2759 97.90% 2.00% 0.14% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.80% 1.80% 0.34% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 96.70% 3.20% 0.11% 0.00% NA
Indica Intermediate  786 98.60% 1.30% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg1205351745 C -> T LOC_Os12g10110.1 upstream_gene_variant ; 1513.0bp to feature; MODIFIER N Average:38.77; most accessible tissue: Minghui63 flag leaf, score: 68.16 N N N N
vg1205351745 C -> T LOC_Os12g10120.1 upstream_gene_variant ; 4625.0bp to feature; MODIFIER N Average:38.77; most accessible tissue: Minghui63 flag leaf, score: 68.16 N N N N
vg1205351745 C -> T LOC_Os12g10100.1 downstream_gene_variant ; 3443.0bp to feature; MODIFIER N Average:38.77; most accessible tissue: Minghui63 flag leaf, score: 68.16 N N N N
vg1205351745 C -> T LOC_Os12g10110-LOC_Os12g10120 intergenic_region ; MODIFIER N Average:38.77; most accessible tissue: Minghui63 flag leaf, score: 68.16 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1205351745 2.19E-06 NA mr1946 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
vg1205351745 4.21E-07 3.09E-07 mr1946 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