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Detailed information for vg0131435897:

Variant ID: vg0131435897 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 31435897
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


CTGCAGTTAAGCCATTTAGCGGATTTGCAAAAATTGAACATAAACTTGCCAATATCATAATAAATTCGTGACAACATCAGAGATTCAAAATAGTTCAAAA[C/T]
ACTTCAATTCTTCAACACTCGACAACATCAAAGCAAGAAATCCTACCTGCCTCTGACTCCGCTAGGACATGGTGCCTGCCGTTCGAGCTTGGTGCCTTGG

Reverse complement sequence

CCAAGGCACCAAGCTCGAACGGCAGGCACCATGTCCTAGCGGAGTCAGAGGCAGGTAGGATTTCTTGCTTTGATGTTGTCGAGTGTTGAAGAATTGAAGT[G/A]
TTTTGAACTATTTTGAATCTCTGATGTTGTCACGAATTTATTATGATATTGGCAAGTTTATGTTCAATTTTTGCAAATCCGCTAAATGGCTTAACTGCAG

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 87.60% 12.40% 0.04% 0.00% NA
All Indica  2759 78.70% 21.20% 0.07% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.80% 4.20% 0.00% 0.00% NA
Indica II  465 97.00% 2.80% 0.22% 0.00% NA
Indica III  913 56.50% 43.40% 0.11% 0.00% NA
Indica Intermediate  786 80.80% 19.20% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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
vg0131435897 C -> T LOC_Os01g54630.1 upstream_gene_variant ; 2695.0bp to feature; MODIFIER silent_mutation Average:29.999; most accessible tissue: Zhenshan97 flag leaf, score: 39.027 N N N N
vg0131435897 C -> T LOC_Os01g54650.1 upstream_gene_variant ; 4475.0bp to feature; MODIFIER silent_mutation Average:29.999; most accessible tissue: Zhenshan97 flag leaf, score: 39.027 N N N N
vg0131435897 C -> T LOC_Os01g54640.1 intron_variant ; MODIFIER silent_mutation Average:29.999; most accessible tissue: Zhenshan97 flag leaf, score: 39.027 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0131435897 6.08E-06 1.30E-06 mr1392 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
vg0131435897 NA 1.35E-06 mr1677 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
vg0131435897 7.74E-06 7.37E-07 mr1677 Ind_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
vg0131435897 3.01E-06 3.01E-06 mr1972 Ind_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
vg0131435897 NA 1.89E-06 mr1723_2 Ind_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