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Detailed information for vg0630863586:

Variant ID: vg0630863586 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 30863586
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, T: 0.08, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


CAAAAGATTCGTCTCGCAGTTTACAGTCCAAATATGTAATTTATTTTGTTATTAGTCTACGTTTAATACTTCAAATGTGTGTCCGTATACGTCAAAAAAA[A/T]
TTTTGACGCCGAACTAAACACGGCTTTTGTTTAAAATGTGCTTGCATGATATTGGCTGAAAATAGATTTTTTTATCATCTCCTATATATATACCTTACAT

Reverse complement sequence

ATGTAAGGTATATATATAGGAGATGATAAAAAAATCTATTTTCAGCCAATATCATGCAAGCACATTTTAAACAAAAGCCGTGTTTAGTTCGGCGTCAAAA[T/A]
TTTTTTTGACGTATACGGACACACATTTGAAGTATTAAACGTAGACTAATAACAAAATAAATTACATATTTGGACTGTAAACTGCGAGACGAATCTTTTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.60% 10.40% 0.02% 0.00% NA
All Indica  2759 98.10% 1.90% 0.00% 0.00% NA
All Japonica  1512 83.10% 16.80% 0.07% 0.00% NA
Aus  269 51.30% 48.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 96.60% 3.40% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 2.40% 0.00% 0.00% NA
Temperate Japonica  767 99.20% 0.80% 0.00% 0.00% NA
Tropical Japonica  504 54.40% 45.40% 0.20% 0.00% NA
Japonica Intermediate  241 92.10% 7.90% 0.00% 0.00% NA
VI/Aromatic  96 54.20% 45.80% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0630863586 A -> T LOC_Os06g51000.1 upstream_gene_variant ; 2427.0bp to feature; MODIFIER silent_mutation Average:42.702; most accessible tissue: Zhenshan97 root, score: 77.09 N N N N
vg0630863586 A -> T LOC_Os06g50990.1 downstream_gene_variant ; 4123.0bp to feature; MODIFIER silent_mutation Average:42.702; most accessible tissue: Zhenshan97 root, score: 77.09 N N N N
vg0630863586 A -> T LOC_Os06g50990-LOC_Os06g51000 intergenic_region ; MODIFIER silent_mutation Average:42.702; most accessible tissue: Zhenshan97 root, score: 77.09 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0630863586 4.72E-06 NA mr1362_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
vg0630863586 NA 4.15E-06 mr1762_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
vg0630863586 2.26E-06 NA mr1836_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