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Detailed information for vg0120412875:

Variant ID: vg0120412875 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 20412875
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


ACCTTCTTTTTGTGATTTCGGCCGACTGGGATGGAATTTGGTGATGAAGCTAGATCCATTGGAAAGATGACTCCGAGAGCTTTCCATCAAGTACTCATGG[T/A]
CCCAAAATGGAGCTCGCATGCATATTTGGTGGCCGTTTAAAGTCGACACTGTAGCAGGTGGCCGAACTGGATTGTAGAACTTGGACGGCTTGATCTTGAT

Reverse complement sequence

ATCAAGATCAAGCCGTCCAAGTTCTACAATCCAGTTCGGCCACCTGCTACAGTGTCGACTTTAAACGGCCACCAAATATGCATGCGAGCTCCATTTTGGG[A/T]
CCATGAGTACTTGATGGAAAGCTCTCGGAGTCATCTTTCCAATGGATCTAGCTTCATCACCAAATTCCATCCCAGTCGGCCGAAATCACAAAAAGAAGGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.30% 11.10% 4.61% 0.00% NA
All Indica  2759 95.00% 2.20% 2.79% 0.00% NA
All Japonica  1512 62.20% 29.50% 8.27% 0.00% NA
Aus  269 95.50% 1.50% 2.97% 0.00% NA
Indica I  595 94.80% 2.20% 3.03% 0.00% NA
Indica II  465 93.10% 2.80% 4.09% 0.00% NA
Indica III  913 99.10% 0.30% 0.55% 0.00% NA
Indica Intermediate  786 91.50% 4.10% 4.45% 0.00% NA
Temperate Japonica  767 38.70% 50.50% 10.82% 0.00% NA
Tropical Japonica  504 92.10% 3.80% 4.17% 0.00% NA
Japonica Intermediate  241 74.70% 16.60% 8.71% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 76.70% 14.40% 8.89% 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
vg0120412875 T -> A LOC_Os01g36740.1 upstream_gene_variant ; 3206.0bp to feature; MODIFIER silent_mutation Average:41.207; most accessible tissue: Minghui63 flag leaf, score: 68.675 N N N N
vg0120412875 T -> A LOC_Os01g36750.1 downstream_gene_variant ; 619.0bp to feature; MODIFIER silent_mutation Average:41.207; most accessible tissue: Minghui63 flag leaf, score: 68.675 N N N N
vg0120412875 T -> A LOC_Os01g36760.1 downstream_gene_variant ; 1441.0bp to feature; MODIFIER silent_mutation Average:41.207; most accessible tissue: Minghui63 flag leaf, score: 68.675 N N N N
vg0120412875 T -> A LOC_Os01g36750-LOC_Os01g36760 intergenic_region ; MODIFIER silent_mutation Average:41.207; most accessible tissue: Minghui63 flag leaf, score: 68.675 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0120412875 NA 1.17E-06 mr1011 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
vg0120412875 9.07E-07 9.06E-07 mr1011 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
vg0120412875 NA 1.17E-08 mr1163 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
vg0120412875 NA 5.22E-13 mr1182 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
vg0120412875 NA 1.49E-06 mr1182 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
vg0120412875 3.21E-06 9.10E-14 mr1650 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
vg0120412875 NA 1.07E-06 mr1650 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
vg0120412875 NA 9.41E-09 mr1658 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
vg0120412875 NA 8.11E-06 mr1808 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
vg0120412875 NA 1.91E-06 mr1977 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
vg0120412875 NA 5.26E-08 mr1010_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
vg0120412875 5.99E-06 2.36E-13 mr1011_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
vg0120412875 NA 1.79E-08 mr1011_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
vg0120412875 NA 5.98E-16 mr1013_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
vg0120412875 NA 8.41E-07 mr1013_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
vg0120412875 NA 8.87E-15 mr1031_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
vg0120412875 NA 6.21E-06 mr1870_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