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Detailed information for vg1221123346:

Variant ID: vg1221123346 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 21123346
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTTCTAAAATTGAGATCTAGATGTTAAAAATATCAACATATACTGTTCATGCTTGTTTATGTGCTGTTTTGGTGATTTTGCTCTTTTCTCTTTAGATT[C/T]
CGACGTTTCCGGAGAGTCCGTTTTTGCAGGAGAAGAATTTGAAGAGTTCCAAGGCCAGCAAGGCAAGTCACACAGATCCCAAACAACCCTTTGAGCATGT

Reverse complement sequence

ACATGCTCAAAGGGTTGTTTGGGATCTGTGTGACTTGCCTTGCTGGCCTTGGAACTCTTCAAATTCTTCTCCTGCAAAAACGGACTCTCCGGAAACGTCG[G/A]
AATCTAAAGAGAAAAGAGCAAAATCACCAAAACAGCACATAAACAAGCATGAACAGTATATGTTGATATTTTTAACATCTAGATCTCAATTTTAGAAAAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 72.50% 27.30% 0.23% 0.00% NA
All Indica  2759 61.00% 38.70% 0.29% 0.00% NA
All Japonica  1512 98.40% 1.60% 0.00% 0.00% NA
Aus  269 37.20% 62.10% 0.74% 0.00% NA
Indica I  595 82.20% 17.80% 0.00% 0.00% NA
Indica II  465 42.80% 57.00% 0.22% 0.00% NA
Indica III  913 56.60% 43.30% 0.11% 0.00% NA
Indica Intermediate  786 60.70% 38.50% 0.76% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 97.00% 3.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 78.90% 20.00% 1.11% 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
vg1221123346 C -> T LOC_Os12g34790.1 missense_variant ; p.Pro25Ser; MODERATE nonsynonymous_codon ; P25L Average:14.15; most accessible tissue: Minghui63 panicle, score: 20.733 probably damaging 2.029 DELETERIOUS 0.00
vg1221123346 C -> T LOC_Os12g34790.1 missense_variant ; p.Pro25Ser; MODERATE nonsynonymous_codon ; P25S Average:14.15; most accessible tissue: Minghui63 panicle, score: 20.733 possibly damaging 1.831 TOLERATED 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1221123346 5.83E-06 1.03E-07 mr1928_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
vg1221123346 NA 4.85E-06 mr1931_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