Search for Variation information by Variation ID:

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

Detailed information for vg1128763670:

Variant ID: vg1128763670 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 28763670
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, G: 0.07, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


TAACTACTCCTATAGCAGAGAAATTAATGCGGAAGTACTTCCATTAAGTCATCCATCACAACACAACTGCATGCTAATTAACATGGCTGTAGTTATTAGT[A/G]
GTTGGTAATCTCCTTTAATTCGCACTCCATAGCTTAGAGATTTCGAACCTACTATGTCAAAATATTAGTAATACCAAAACCTAGCTAAGTTTTGATAATG

Reverse complement sequence

CATTATCAAAACTTAGCTAGGTTTTGGTATTACTAATATTTTGACATAGTAGGTTCGAAATCTCTAAGCTATGGAGTGCGAATTAAAGGAGATTACCAAC[T/C]
ACTAATAACTACAGCCATGTTAATTAGCATGCAGTTGTGTTGTGATGGATGACTTAATGGAAGTACTTCCGCATTAATTTCTCTGCTATAGGAGTAGTTA

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 73.50% 26.20% 0.28% 0.00% NA
All Indica  2759 61.80% 38.00% 0.25% 0.00% NA
All Japonica  1512 93.80% 6.00% 0.20% 0.00% NA
Aus  269 67.70% 32.00% 0.37% 0.00% NA
Indica I  595 74.80% 24.90% 0.34% 0.00% NA
Indica II  465 31.00% 68.80% 0.22% 0.00% NA
Indica III  913 74.20% 25.70% 0.11% 0.00% NA
Indica Intermediate  786 55.70% 43.90% 0.38% 0.00% NA
Temperate Japonica  767 90.00% 9.60% 0.39% 0.00% NA
Tropical Japonica  504 98.00% 2.00% 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 84.40% 13.30% 2.22% 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
vg1128763670 A -> G LOC_Os11g47600.1 upstream_gene_variant ; 3663.0bp to feature; MODIFIER silent_mutation Average:58.716; most accessible tissue: Zhenshan97 root, score: 79.962 N N N N
vg1128763670 A -> G LOC_Os11g47610.1 upstream_gene_variant ; 2067.0bp to feature; MODIFIER silent_mutation Average:58.716; most accessible tissue: Zhenshan97 root, score: 79.962 N N N N
vg1128763670 A -> G LOC_Os11g47620.1 upstream_gene_variant ; 448.0bp to feature; MODIFIER silent_mutation Average:58.716; most accessible tissue: Zhenshan97 root, score: 79.962 N N N N
vg1128763670 A -> G LOC_Os11g47630.1 downstream_gene_variant ; 2422.0bp to feature; MODIFIER silent_mutation Average:58.716; most accessible tissue: Zhenshan97 root, score: 79.962 N N N N
vg1128763670 A -> G LOC_Os11g47620-LOC_Os11g47630 intergenic_region ; MODIFIER silent_mutation Average:58.716; most accessible tissue: Zhenshan97 root, score: 79.962 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1128763670 NA 6.64E-06 mr1268 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
vg1128763670 8.97E-06 NA mr1517 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
vg1128763670 6.91E-07 1.67E-06 mr1962 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
vg1128763670 NA 7.57E-09 mr1191_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