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Detailed information for vg0138861491:

Variant ID: vg0138861491 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 38861491
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: 57. )

Flanking Sequence (100 bp) in Reference Genome:


AGATCTCTGCTCCTCCTAGAGTATAGTCCCGGTCCTCACCATTGACCAAGGCTGACCTCAAGTCACCTGCACACAATCAGACAAAACAACCGTTTCTGGG[C/T]
ACAGATATCACAACCTGACCCACATTAGTCACACACACTCACACCAACATTCACACATACTCTCAAACCAATTCTTTGATTAAATCATTTGCATAGCCAA

Reverse complement sequence

TTGGCTATGCAAATGATTTAATCAAAGAATTGGTTTGAGAGTATGTGTGAATGTTGGTGTGAGTGTGTGTGACTAATGTGGGTCAGGTTGTGATATCTGT[G/A]
CCCAGAAACGGTTGTTTTGTCTGATTGTGTGCAGGTGACTTGAGGTCAGCCTTGGTCAATGGTGAGGACCGGGACTATACTCTAGGAGGAGCAGAGATCT

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 40.70% 2.80% 17.60% 38.98% NA
All Indica  2759 14.20% 4.50% 27.40% 53.90% NA
All Japonica  1512 92.70% 0.20% 1.85% 5.29% NA
Aus  269 3.70% 0.00% 8.92% 87.36% NA
Indica I  595 13.60% 0.50% 18.32% 67.56% NA
Indica II  465 10.30% 5.20% 13.55% 70.97% NA
Indica III  913 18.10% 6.50% 43.04% 32.42% NA
Indica Intermediate  786 12.30% 5.00% 24.30% 58.40% NA
Temperate Japonica  767 97.10% 0.00% 0.65% 2.22% NA
Tropical Japonica  504 85.50% 0.40% 4.17% 9.92% NA
Japonica Intermediate  241 93.40% 0.40% 0.83% 5.39% NA
VI/Aromatic  96 75.00% 0.00% 9.38% 15.62% NA
Intermediate  90 53.30% 2.20% 16.67% 27.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0138861491 C -> T LOC_Os01g66910.1 upstream_gene_variant ; 1277.0bp to feature; MODIFIER silent_mutation Average:45.092; most accessible tissue: Callus, score: 68.402 N N N N
vg0138861491 C -> T LOC_Os01g66920.1 upstream_gene_variant ; 2529.0bp to feature; MODIFIER silent_mutation Average:45.092; most accessible tissue: Callus, score: 68.402 N N N N
vg0138861491 C -> T LOC_Os01g66910-LOC_Os01g66920 intergenic_region ; MODIFIER silent_mutation Average:45.092; most accessible tissue: Callus, score: 68.402 N N N N
vg0138861491 C -> DEL N N silent_mutation Average:45.092; most accessible tissue: Callus, score: 68.402 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0138861491 NA 5.81E-06 mr1138_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
vg0138861491 5.35E-06 5.35E-06 mr1799_2 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
vg0138861491 NA 7.39E-06 mr1869_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
vg0138861491 9.68E-07 9.72E-07 mr1956_2 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
vg0138861491 NA 1.82E-06 mr1956_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