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Detailed information for vg1213914515:

Variant ID: vg1213914515 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 13914515
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


CGGGGCGAGCTCGACGGAATCGTCAAATCCCTCATTGCCAACGGTGGCACCGACATCAAGGCCGGCCTTGACTTGGGGCTGGCTGTCCTCGCCGACCGCG[T/C]
GTTCACGGAATCCCGCACCGCCAACATCTTCCTCATGTCCGACGGCAAGCTCGAGGGTAAGACCTCCGGTGACCCGACGCAAGTCAACCCCGGCGAGGTC

Reverse complement sequence

GACCTCGCCGGGGTTGACTTGCGTCGGGTCACCGGAGGTCTTACCCTCGAGCTTGCCGTCGGACATGAGGAAGATGTTGGCGGTGCGGGATTCCGTGAAC[A/G]
CGCGGTCGGCGAGGACAGCCAGCCCCAAGTCAAGGCCGGCCTTGATGTCGGTGCCACCGTTGGCAATGAGGGATTTGACGATTCCGTCGAGCTCGCCCCG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.60% 9.30% 0.06% 0.00% NA
All Indica  2759 84.30% 15.50% 0.11% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 56.00% 43.50% 0.50% 0.00% NA
Indica II  465 95.30% 4.70% 0.00% 0.00% NA
Indica III  913 95.40% 4.60% 0.00% 0.00% NA
Indica Intermediate  786 86.50% 13.50% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg1213914515 T -> C LOC_Os12g24390.1 missense_variant ; p.Val154Ala; MODERATE nonsynonymous_codon ; V154T Average:77.969; most accessible tissue: Zhenshan97 young leaf, score: 90.27 unknown unknown TOLERATED 0.60

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1213914515 NA 2.90E-06 mr1308 Ind_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
vg1213914515 NA 3.92E-06 mr1164_2 Ind_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
vg1213914515 NA 1.92E-06 mr1170_2 Ind_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
vg1213914515 NA 1.08E-07 mr1308_2 Ind_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
vg1213914515 NA 2.45E-08 mr1361_2 Ind_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
vg1213914515 NA 2.62E-06 mr1745_2 Ind_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