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Detailed information for vg0508461245:

Variant ID: vg0508461245 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 8461245
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


GGATAGGGATAACCACTCGTCTCATGGGCAAACGGAATATTTTTTGAACAAACCTACGAACGGGTAATCACACTCTCGTGACAAGGACGGACGGCTTTCA[A/G]
CATAAACCGATGAAGATGGATGAAAACTAGACTAGAACTAAGTAAAAAGTAGATGTGATAATGAAAAATGATTCAATTGGCTAATTGTGTTAAAATTAGA

Reverse complement sequence

TCTAATTTTAACACAATTAGCCAATTGAATCATTTTTCATTATCACATCTACTTTTTACTTAGTTCTAGTCTAGTTTTCATCCATCTTCATCGGTTTATG[T/C]
TGAAAGCCGTCCGTCCTTGTCACGAGAGTGTGATTACCCGTTCGTAGGTTTGTTCAAAAAATATTCCGTTTGCCCATGAGACGAGTGGTTATCCCTATCC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.70% 10.20% 3.13% 0.00% NA
All Indica  2759 97.30% 1.00% 1.67% 0.00% NA
All Japonica  1512 64.20% 29.40% 6.42% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 92.30% 2.70% 5.04% 0.00% NA
Indica II  465 96.60% 1.70% 1.72% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.60% 0.40% 1.02% 0.00% NA
Temperate Japonica  767 35.90% 55.50% 8.60% 0.00% NA
Tropical Japonica  504 96.60% 0.40% 2.98% 0.00% NA
Japonica Intermediate  241 86.30% 7.10% 6.64% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 87.80% 7.80% 4.44% 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
vg0508461245 A -> G LOC_Os05g14890.1 downstream_gene_variant ; 4275.0bp to feature; MODIFIER silent_mutation Average:57.905; most accessible tissue: Callus, score: 74.734 N N N N
vg0508461245 A -> G LOC_Os05g14900.1 intron_variant ; MODIFIER silent_mutation Average:57.905; most accessible tissue: Callus, score: 74.734 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0508461245 NA 2.67E-07 mr1026 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
vg0508461245 NA 2.16E-30 mr1137 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
vg0508461245 NA 8.09E-12 mr1137 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
vg0508461245 NA 5.03E-06 mr1164 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
vg0508461245 NA 3.41E-06 mr1330 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
vg0508461245 NA 7.35E-06 mr1380 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
vg0508461245 NA 3.82E-27 mr1617 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
vg0508461245 NA 3.16E-11 mr1617 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
vg0508461245 NA 6.32E-11 mr1627 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
vg0508461245 NA 3.06E-06 mr1937 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
vg0508461245 NA 2.56E-07 mr1977 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
vg0508461245 NA 1.65E-06 mr1977 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
vg0508461245 4.46E-09 1.85E-38 mr1137_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
vg0508461245 NA 6.17E-14 mr1137_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
vg0508461245 8.64E-07 8.17E-27 mr1617_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
vg0508461245 NA 2.81E-10 mr1617_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