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Detailed information for vg0129406641:

Variant ID: vg0129406641 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 29406641
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:


AATGATGTTAGAATATTTGAATTTTGTCTTGTGTCTGTTCATGGGATAACATAATATCTGCAAAAGTTCAATTGGTGGAATGGATTCATTCGTTATGTGG[T/A]
TTTGCCCATAGATGCTGCTACAAGTTCAGAAGAGAAGAATTATGGTGCTGTTGTCTGTGGGTATGGTCATAGTGGATTGAAACTAGCAGGACAGACAGGA

Reverse complement sequence

TCCTGTCTGTCCTGCTAGTTTCAATCCACTATGACCATACCCACAGACAACAGCACCATAATTCTTCTCTTCTGAACTTGTAGCAGCATCTATGGGCAAA[A/T]
CCACATAACGAATGAATCCATTCCACCAATTGAACTTTTGCAGATATTATGTTATCCCATGAACAGACACAAGACAAAATTCAAATATTCTAACATCATT

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 97.40% 1.80% 0.78% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 92.10% 5.60% 2.31% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 93.10% 4.30% 2.61% 0.00% NA
Tropical Japonica  504 97.80% 2.00% 0.20% 0.00% NA
Japonica Intermediate  241 76.80% 17.40% 5.81% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 2.20% 2.22% 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
vg0129406641 T -> A LOC_Os01g51154.1 intron_variant ; MODIFIER silent_mutation Average:58.338; most accessible tissue: Minghui63 flower, score: 73.443 N N N N
vg0129406641 T -> A LOC_Os01g51154.3 intron_variant ; MODIFIER silent_mutation Average:58.338; most accessible tissue: Minghui63 flower, score: 73.443 N N N N
vg0129406641 T -> A LOC_Os01g51154.2 intron_variant ; MODIFIER silent_mutation Average:58.338; most accessible tissue: Minghui63 flower, score: 73.443 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0129406641 2.01E-06 6.65E-06 mr1276 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
vg0129406641 2.76E-06 2.76E-06 mr1904 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
vg0129406641 1.66E-06 1.66E-06 mr1987 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