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Detailed information for vg1222740003:

Variant ID: vg1222740003 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 22740003
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


TTAGGTAAATGATATGAACCCATGTTTCCCAATGCTATCTTTTTGATTTAACGATGACAAAAAAAAAGAGATATTGAAGTGAACCAATGTTATCGGTAAC[G/T]
CTATTCCGCGCTGTATTAGTTCGAGTGCCGCACAGCGTCCTCTGTTTTTCCCTTTTTTACCACCTCATCTTTCCTATGCATCCCACCTTTTCTCAGTTCG

Reverse complement sequence

CGAACTGAGAAAAGGTGGGATGCATAGGAAAGATGAGGTGGTAAAAAAGGGAAAAACAGAGGACGCTGTGCGGCACTCGAACTAATACAGCGCGGAATAG[C/A]
GTTACCGATAACATTGGTTCACTTCAATATCTCTTTTTTTTTGTCATCGTTAAATCAAAAAGATAGCATTGGGAAACATGGGTTCATATCATTTACCTAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.10% 6.60% 0.02% 1.21% NA
All Indica  2759 86.60% 11.30% 0.04% 2.07% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.60% 3.40% 0.00% 0.00% NA
Indica II  465 89.90% 2.80% 0.22% 7.10% NA
Indica III  913 79.00% 20.60% 0.00% 0.44% NA
Indica Intermediate  786 86.00% 11.50% 0.00% 2.54% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1222740003 G -> DEL N N silent_mutation Average:37.003; most accessible tissue: Zhenshan97 young leaf, score: 67.334 N N N N
vg1222740003 G -> T LOC_Os12g37120.1 upstream_gene_variant ; 3335.0bp to feature; MODIFIER silent_mutation Average:37.003; most accessible tissue: Zhenshan97 young leaf, score: 67.334 N N N N
vg1222740003 G -> T LOC_Os12g37110-LOC_Os12g37120 intergenic_region ; MODIFIER silent_mutation Average:37.003; most accessible tissue: Zhenshan97 young leaf, score: 67.334 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1222740003 4.49E-06 4.49E-06 mr1373 Ind_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