Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1221699222:

Variant ID: vg1221699222 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 21699222
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


GGATGTCACGTGGTGACTTAAGTGCATTCGTTTAATGGACTTGTGCGTAGAATACAACTTGAAATAACATATATTTTTTTACAACTATTAGCTGAAATTA[T/A]
TAATTTGGTTTTTATCTCCCATGAGTGAAAAAAAGAAAAAAGAAAAGAAGGGAAGGGGGGACACGTACGTACGAAGTATATACGTACATGCACGTACACG

Reverse complement sequence

CGTGTACGTGCATGTACGTATATACTTCGTACGTACGTGTCCCCCCTTCCCTTCTTTTCTTTTTTCTTTTTTTCACTCATGGGAGATAAAAACCAAATTA[A/T]
TAATTTCAGCTAATAGTTGTAAAAAAATATATGTTATTTCAAGTTGTATTCTACGCACAAGTCCATTAAACGAATGCACTTAAGTCACCACGTGACATCC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.50% 8.40% 0.11% 0.00% NA
All Indica  2759 93.50% 6.30% 0.14% 0.00% NA
All Japonica  1512 95.80% 4.20% 0.00% 0.00% NA
Aus  269 44.20% 55.40% 0.37% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 96.30% 3.00% 0.65% 0.00% NA
Indica III  913 88.30% 11.60% 0.11% 0.00% NA
Indica Intermediate  786 93.30% 6.70% 0.00% 0.00% NA
Temperate Japonica  767 97.30% 2.70% 0.00% 0.00% NA
Tropical Japonica  504 92.90% 7.10% 0.00% 0.00% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg1221699222 T -> A LOC_Os12g35680.1 upstream_gene_variant ; 3624.0bp to feature; MODIFIER silent_mutation Average:42.759; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg1221699222 T -> A LOC_Os12g35690.1 upstream_gene_variant ; 636.0bp to feature; MODIFIER silent_mutation Average:42.759; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg1221699222 T -> A LOC_Os12g35700.1 downstream_gene_variant ; 3203.0bp to feature; MODIFIER silent_mutation Average:42.759; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg1221699222 T -> A LOC_Os12g35680-LOC_Os12g35690 intergenic_region ; MODIFIER silent_mutation Average:42.759; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1221699222 4.84E-06 9.09E-07 mr1676 Jap_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
vg1221699222 NA 6.33E-06 mr1236_2 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
vg1221699222 2.90E-07 2.31E-10 mr1676_2 Jap_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