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Detailed information for vg0311297814:

Variant ID: vg0311297814 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 11297814
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 168. )

Flanking Sequence (100 bp) in Reference Genome:


ACATGACCGGGCGAAGCACGCGCTAAAGTCCGCCCCTCACGGCAAGATAATCAAGATGCAGATTGATGACGCCGACCCCACAAAGCTCGTATCGCTGGGG[G/C]
GCGACATGGGCGAAGAAGAGGCTGCGAACATTCTAGAGGTACTCAAGAAAAATAGTGATATCTTCGCCTAGGGCCCTAATCAAGTGGGAGGTGTTTCGAT

Reverse complement sequence

ATCGAAACACCTCCCACTTGATTAGGGCCCTAGGCGAAGATATCACTATTTTTCTTGAGTACCTCTAGAATGTTCGCAGCCTCTTCTTCGCCCATGTCGC[C/G]
CCCCAGCGATACGAGCTTTGTGGGGTCGGCGTCATCAATCTGCATCTTGATTATCTTGCCGTGAGGGGCGGACTTTAGCGCGTGCTTCGCCCGGTCATGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.50% 0.10% 1.42% 5.97% NA
All Indica  2759 87.20% 0.10% 2.43% 10.22% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 87.10% 0.20% 2.02% 10.76% NA
Indica II  465 69.90% 0.00% 5.38% 24.73% NA
Indica III  913 95.80% 0.10% 1.10% 2.96% NA
Indica Intermediate  786 87.70% 0.10% 2.54% 9.67% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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
vg0311297814 G -> C LOC_Os03g20050.1 missense_variant ; p.Gly152Arg; MODERATE nonsynonymous_codon ; G152R Average:51.402; most accessible tissue: Minghui63 flag leaf, score: 68.16 unknown unknown TOLERATED 0.78
vg0311297814 G -> DEL LOC_Os03g20050.1 N frameshift_variant Average:51.402; most accessible tissue: Minghui63 flag leaf, score: 68.16 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0311297814 3.12E-06 5.03E-08 mr1748_2 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