Search for Variation information by Variation ID:

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

Detailed information for vg0306588571:

Variant ID: vg0306588571 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 6588571
Reference Allele: CAlternative Allele: T,CT
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


TCATGGACTAATTAGGCTCAAGCAATTAGTTTTTGTTTTTATCTATATTTAATGCTTCATGCATATGTTTAAAGATTTGATGTGATGTTTTTGGGAAAAA[C/T,CT]
TTTTTGGAAACTAAACAGGGCCTTACTCCATTCATTTTTATGACAATCATTTTGGTGTCCTTAATTTCCACGAGCACGTCTTGTTTGTCCTGTTATGACA

Reverse complement sequence

TGTCATAACAGGACAAACAAGACGTGCTCGTGGAAATTAAGGACACCAAAATGATTGTCATAAAAATGAATGGAGTAAGGCCCTGTTTAGTTTCCAAAAA[G/A,AG]
TTTTTCCCAAAAACATCACATCAAATCTTTAAACATATGCATGAAGCATTAAATATAGATAAAAACAAAAACTAATTGCTTGAGCCTAATTAGTCCATGA

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 98.20% 1.20% 0.53% 0.00% CT: 0.06%
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 94.60% 3.60% 1.65% 0.00% CT: 0.07%
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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 89.60% 7.20% 3.26% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.00% 0.00% CT: 0.20%
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% 0.00% 0.00% 0.00% CT: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0306588571 C -> T LOC_Os03g12470.1 upstream_gene_variant ; 1100.0bp to feature; MODIFIER silent_mutation Average:73.389; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0306588571 C -> T LOC_Os03g12460.1 downstream_gene_variant ; 704.0bp to feature; MODIFIER silent_mutation Average:73.389; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0306588571 C -> T LOC_Os03g12460-LOC_Os03g12470 intergenic_region ; MODIFIER silent_mutation Average:73.389; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0306588571 C -> CT LOC_Os03g12470.1 upstream_gene_variant ; 1099.0bp to feature; MODIFIER silent_mutation Average:73.389; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0306588571 C -> CT LOC_Os03g12460.1 downstream_gene_variant ; 705.0bp to feature; MODIFIER silent_mutation Average:73.389; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0306588571 C -> CT LOC_Os03g12460-LOC_Os03g12470 intergenic_region ; MODIFIER silent_mutation Average:73.389; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0306588571 4.61E-06 4.61E-06 mr1283 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
vg0306588571 NA 4.59E-06 mr1358 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
vg0306588571 NA 4.04E-06 mr1712 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