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Detailed information for vg1221032304:

Variant ID: vg1221032304 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 21032304
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGTAAAAGCCGTCTTAGGTATATCTTCCTCTTTAATCCTCAACTGGTGATACCCCGATCGAAGATCGATTTTGGAGAAAACGGTGGCTCCTTTAAGCTG[A/G]
TCAAACAAATCATCAATTCTAGGCAGAGGGTACTTATTCTTGATGGTCACATCATTTAGTGCACGATAATCCATACACATCCTCTGGGTATGATCTTTCT

Reverse complement sequence

AGAAAGATCATACCCAGAGGATGTGTATGGATTATCGTGCACTAAATGATGTGACCATCAAGAATAAGTACCCTCTGCCTAGAATTGATGATTTGTTTGA[T/C]
CAGCTTAAAGGAGCCACCGTTTTCTCCAAAATCGATCTTCGATCGGGGTATCACCAGTTGAGGATTAAAGAGGAAGATATACCTAAGACGGCTTTTACCA

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 94.80% 3.20% 2.01% 0.00% NA
All Indica  2759 92.10% 4.70% 3.23% 0.00% NA
All Japonica  1512 99.70% 0.20% 0.07% 0.00% NA
Aus  269 92.90% 5.60% 1.49% 0.00% NA
Indica I  595 99.20% 0.50% 0.34% 0.00% NA
Indica II  465 93.80% 4.90% 1.29% 0.00% NA
Indica III  913 86.30% 7.30% 6.35% 0.00% NA
Indica Intermediate  786 92.40% 4.70% 2.93% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.60% 0.20% 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 97.80% 1.10% 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
vg1221032304 A -> G LOC_Os12g34650.1 synonymous_variant ; p.Asp893Asp; LOW synonymous_codon Average:41.935; most accessible tissue: Minghui63 flag leaf, score: 67.635 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1221032304 5.71E-06 NA mr1952 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
vg1221032304 2.94E-06 1.07E-06 mr1952 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