Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg1000480049:

Variant ID: vg1000480049 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 480049
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTTTCAAAGTAGTTTTTAACTTTTAGGAGTAGCGTTTACACTTTCGGAGGCATTGTGAAATGGTATATTTGCAAACGAAAAGTAATTGTGAATAAAAA[T/A]
TTTATATACGTGTCTTTAGCGATCTAAAAGTAAAGGCTGAAAAATAAACTTCGATGAAAAATCCTTAAAATCAACTCCAAATGTAAGGTTAAAATTTAAA

Reverse complement sequence

TTTAAATTTTAACCTTACATTTGGAGTTGATTTTAAGGATTTTTCATCGAAGTTTATTTTTCAGCCTTTACTTTTAGATCGCTAAAGACACGTATATAAA[A/T]
TTTTTATTCACAATTACTTTTCGTTTGCAAATATACCATTTCACAATGCCTCCGAAAGTGTAAACGCTACTCCTAAAAGTTAAAAACTACTTTGAAAAAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.20% 0.80% 0.30% 0.72% NA
All Indica  2759 99.80% 0.00% 0.00% 0.22% NA
All Japonica  1512 96.80% 2.40% 0.86% 0.00% NA
Aus  269 89.20% 0.00% 0.37% 10.41% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.00% 0.00% 0.76% NA
Temperate Japonica  767 94.40% 4.20% 1.43% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 1.70% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1000480049 T -> A LOC_Os10g01740.1 upstream_gene_variant ; 2217.0bp to feature; MODIFIER silent_mutation Average:38.497; most accessible tissue: Callus, score: 71.455 N N N N
vg1000480049 T -> A LOC_Os10g01730.1 downstream_gene_variant ; 3995.0bp to feature; MODIFIER silent_mutation Average:38.497; most accessible tissue: Callus, score: 71.455 N N N N
vg1000480049 T -> A LOC_Os10g01750.1 downstream_gene_variant ; 2635.0bp to feature; MODIFIER silent_mutation Average:38.497; most accessible tissue: Callus, score: 71.455 N N N N
vg1000480049 T -> A LOC_Os10g01740-LOC_Os10g01750 intergenic_region ; MODIFIER silent_mutation Average:38.497; most accessible tissue: Callus, score: 71.455 N N N N
vg1000480049 T -> DEL N N silent_mutation Average:38.497; most accessible tissue: Callus, score: 71.455 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1000480049 8.08E-07 2.19E-10 mr1757 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
vg1000480049 6.32E-07 6.97E-10 mr1549_2 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
vg1000480049 9.43E-06 3.48E-07 mr1550_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
vg1000480049 8.32E-06 9.86E-09 mr1757_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