Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1117462451:

Variant ID: vg1117462451 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17462451
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, A: 0.20, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


GTGATATCTCCTAATACCAGTGCTAAAGAATTGTAGAGGTCACGGTCTATCTTGGCTCCGCAGCAATTGTCAAATTTCATAGTATTGGTACCAACAATAA[G/A]
ATGATTTTTCTAATTAAAATTCAAATTAGACCCTCTATATATGTTGGCCGGTTACCTTGACAACCTCAAATATCGTAAATTTTAGAGATCTGCTCCGGTC

Reverse complement sequence

GACCGGAGCAGATCTCTAAAATTTACGATATTTGAGGTTGTCAAGGTAACCGGCCAACATATATAGAGGGTCTAATTTGAATTTTAATTAGAAAAATCAT[C/T]
TTATTGTTGGTACCAATACTATGAAATTTGACAATTGCTGCGGAGCCAAGATAGACCGTGACCTCTACAATTCTTTAGCACTGGTATTAGGAGATATCAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.90% 39.10% 0.44% 2.50% NA
All Indica  2759 82.60% 16.80% 0.54% 0.00% NA
All Japonica  1512 8.60% 83.40% 0.26% 7.74% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 83.50% 16.10% 0.34% 0.00% NA
Indica II  465 76.80% 23.20% 0.00% 0.00% NA
Indica III  913 85.20% 14.80% 0.00% 0.00% NA
Indica Intermediate  786 82.40% 15.90% 1.65% 0.00% NA
Temperate Japonica  767 2.10% 82.30% 0.52% 15.12% NA
Tropical Japonica  504 17.90% 81.90% 0.00% 0.20% NA
Japonica Intermediate  241 10.00% 90.00% 0.00% 0.00% NA
VI/Aromatic  96 28.10% 71.90% 0.00% 0.00% NA
Intermediate  90 51.10% 45.60% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1117462451 G -> A LOC_Os11g30020.1 intron_variant ; MODIFIER silent_mutation Average:49.395; most accessible tissue: Minghui63 root, score: 64.607 N N N N
vg1117462451 G -> DEL N N silent_mutation Average:49.395; most accessible tissue: Minghui63 root, score: 64.607 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117462451 3.80E-06 1.07E-06 mr1182 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
vg1117462451 NA 6.31E-06 mr1282 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
vg1117462451 3.03E-06 1.46E-06 mr1650 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
vg1117462451 7.85E-06 3.84E-06 mr1658 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
vg1117462451 NA 6.10E-07 mr1915_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