Search for Variation information by Variation ID:

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

Detailed information for vg1211242175:

Variant ID: vg1211242175 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 11242175
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACCATATATTTATAATGAAGAGTTAACCACTACATGAATAAACTGAGAGATAGACTATATACAATAAACAACTGCTTAGGGTTCACAATTCCGATGAAAA[C/A]
CAGTTGAATTCCGTGAAATTTTGACGTTTCGACACGGCTCGGAATTAAGTTTCGATTGGAATTTTGAAGGTTAAACAGTAGATTTTGTCAAAATTCAGTT

Reverse complement sequence

AACTGAATTTTGACAAAATCTACTGTTTAACCTTCAAAATTCCAATCGAAACTTAATTCCGAGCCGTGTCGAAACGTCAAAATTTCACGGAATTCAACTG[G/T]
TTTTCATCGGAATTGTGAACCCTAAGCAGTTGTTTATTGTATATAGTCTATCTCTCAGTTTATTCATGTAGTGGTTAACTCTTCATTATAAATATATGGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.40% 0.70% 0.85% 0.00% NA
All Indica  2759 99.80% 0.10% 0.11% 0.00% NA
All Japonica  1512 95.40% 2.20% 2.45% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.30% 0.25% 0.00% NA
Temperate Japonica  767 91.30% 4.30% 4.43% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 0.00% 1.24% 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
vg1211242175 C -> A LOC_Os12g19370.1 upstream_gene_variant ; 396.0bp to feature; MODIFIER silent_mutation Average:55.49; most accessible tissue: Callus, score: 76.176 N N N N
vg1211242175 C -> A LOC_Os12g19350-LOC_Os12g19370 intergenic_region ; MODIFIER silent_mutation Average:55.49; most accessible tissue: Callus, score: 76.176 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1211242175 NA 5.96E-06 mr1028 Jap_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
vg1211242175 NA 5.68E-06 mr1652 Jap_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
vg1211242175 9.87E-07 9.87E-07 mr1915 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