Search for Variation information by Variation ID:

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

Detailed information for vg0211863144:

Variant ID: vg0211863144 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 11863144
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.12, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


CACAATAGTTCGATGTGAATTGGAGTGTGACCTAAGCACAACCATAGAGCTGGAGAATAAAGGGAGGACCATGAGAGGAGGGAAAGTGGAGTGAGACACC[G/A]
AGGAGGGCGGAGCAGGGGAGAACGATATGGAAGGCAGGATGCATTTGACGACCTAGGAGTTCCAAAAGCGATGCCTTCAAGAAGGGAACAACATCGGAAT

Reverse complement sequence

ATTCCGATGTTGTTCCCTTCTTGAAGGCATCGCTTTTGGAACTCCTAGGTCGTCAAATGCATCCTGCCTTCCATATCGTTCTCCCCTGCTCCGCCCTCCT[C/T]
GGTGTCTCACTCCACTTTCCCTCCTCTCATGGTCCTCCCTTTATTCTCCAGCTCTATGGTTGTGCTTAGGTCACACTCCAATTCACATCGAACTATTGTG

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 63.80% 35.60% 0.59% 0.00% NA
All Indica  2759 95.70% 3.90% 0.40% 0.00% NA
All Japonica  1512 10.80% 88.10% 1.12% 0.00% NA
Aus  269 61.70% 38.30% 0.00% 0.00% NA
Indica I  595 99.00% 0.50% 0.50% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 94.50% 5.10% 0.33% 0.00% NA
Indica Intermediate  786 93.40% 6.00% 0.64% 0.00% NA
Temperate Japonica  767 1.30% 98.20% 0.52% 0.00% NA
Tropical Japonica  504 26.60% 71.00% 2.38% 0.00% NA
Japonica Intermediate  241 7.90% 91.70% 0.41% 0.00% NA
VI/Aromatic  96 0.00% 100.00% 0.00% 0.00% NA
Intermediate  90 50.00% 50.00% 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
vg0211863144 G -> A LOC_Os02g20130.1 upstream_gene_variant ; 2162.0bp to feature; MODIFIER silent_mutation Average:60.922; most accessible tissue: Zhenshan97 young leaf, score: 80.325 N N N N
vg0211863144 G -> A LOC_Os02g20140.1 intron_variant ; MODIFIER silent_mutation Average:60.922; most accessible tissue: Zhenshan97 young leaf, score: 80.325 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0211863144 NA 5.44E-48 mr1125 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
vg0211863144 NA 6.47E-34 mr1733 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
vg0211863144 9.72E-06 1.55E-06 mr1517_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
vg0211863144 4.13E-06 1.23E-10 mr1538_2 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
vg0211863144 9.54E-06 9.53E-06 mr1541_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