Search for Variation information by Variation ID:

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

Detailed information for vg1105862690:

Variant ID: vg1105862690 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5862690
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATGGTTCCTTACTTATTAAAAGTTACCTCTATGTGAGTTGACATATTATATATCTTAAGTGAATGACTATATCCAAGGAAATATTGACCACATCTTATT[A/G]
AAGGAAATACTGTAGGGGTCTCAGATAATTTTTGGTTCACCTCAATCAGATTTAAAATGATTTTAATGTGAATTTTGAAAGTTTGGCCACTTTAAAAGAA

Reverse complement sequence

TTCTTTTAAAGTGGCCAAACTTTCAAAATTCACATTAAAATCATTTTAAATCTGATTGAGGTGAACCAAAAATTATCTGAGACCCCTACAGTATTTCCTT[T/C]
AATAAGATGTGGTCAATATTTCCTTGGATATAGTCATTCACTTAAGATATATAATATGTCAACTCACATAGAGGTAACTTTTAATAAGTAAGGAACCATA

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 90.40% 9.60% 0.04% 0.00% NA
All Indica  2759 92.60% 7.30% 0.04% 0.00% NA
All Japonica  1512 99.00% 1.00% 0.00% 0.00% NA
Aus  269 16.70% 83.30% 0.00% 0.00% NA
Indica I  595 97.50% 2.50% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 86.50% 13.50% 0.00% 0.00% NA
Indica Intermediate  786 92.50% 7.40% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 97.00% 3.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 6.20% 1.04% 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
vg1105862690 A -> G LOC_Os11g10670-LOC_Os11g10710 intergenic_region ; MODIFIER silent_mutation Average:24.488; most accessible tissue: Callus, score: 57.761 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105862690 NA 9.49E-07 mr1126 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
vg1105862690 NA 1.53E-06 mr1420 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
vg1105862690 NA 3.67E-06 mr1445 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
vg1105862690 NA 7.75E-06 mr1545 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
vg1105862690 NA 1.36E-06 mr1556 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
vg1105862690 4.04E-06 NA mr1970 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