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Detailed information for vg0725311495:

Variant ID: vg0725311495 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 25311495
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, A: 0.02, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


ACCGAATGCGATGCGCGACGGTGTAATTCTGAACGAAGATCAAACGTCGACTGGCTGGCTAGTTCAATCATTATTGGATTTGAGCTGAAAATAGGAGAAA[T/A]
TTTCAAGCTCTGTTATCTTTTTCTTTTTTTCAGATTTCAGATACAGTTGGTGTACGTTTCACCATATAGTACTACTCCCCCCAATGTATACTCCATTTCC

Reverse complement sequence

GGAAATGGAGTATACATTGGGGGGAGTAGTACTATATGGTGAAACGTACACCAACTGTATCTGAAATCTGAAAAAAAGAAAAAGATAACAGAGCTTGAAA[A/T]
TTTCTCCTATTTTCAGCTCAAATCCAATAATGATTGAACTAGCCAGCCAGTCGACGTTTGATCTTCGTTCAGAATTACACCGTCGCGCATCGCATTCGGT

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 55.50% 44.40% 0.13% 0.00% NA
All Indica  2759 25.70% 74.20% 0.07% 0.00% NA
All Japonica  1512 98.70% 1.10% 0.26% 0.00% NA
Aus  269 93.70% 6.30% 0.00% 0.00% NA
Indica I  595 9.60% 90.40% 0.00% 0.00% NA
Indica II  465 24.10% 75.90% 0.00% 0.00% NA
Indica III  913 34.10% 65.80% 0.11% 0.00% NA
Indica Intermediate  786 29.30% 70.60% 0.13% 0.00% NA
Temperate Japonica  767 99.30% 0.30% 0.39% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 93.80% 5.80% 0.41% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 81.10% 18.90% 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
vg0725311495 T -> A LOC_Os07g42290.1 3_prime_UTR_variant ; 365.0bp to feature; MODIFIER silent_mutation Average:54.723; most accessible tissue: Callus, score: 87.925 N N N N
vg0725311495 T -> A LOC_Os07g42300.1 downstream_gene_variant ; 2833.0bp to feature; MODIFIER silent_mutation Average:54.723; most accessible tissue: Callus, score: 87.925 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0725311495 NA 2.46E-34 mr1221_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
vg0725311495 NA 5.91E-07 mr1623_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
vg0725311495 NA 7.74E-13 mr1734_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
vg0725311495 NA 2.22E-07 mr1834_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
vg0725311495 NA 1.56E-17 mr1870_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