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Detailed information for vg1106565379:

Variant ID: vg1106565379 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 6565379
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCTGTGGTTGCTCTCTCACCAACAACCGAGGATTAATTAATTGACCCGGTGTCGATGATGGTGCAGCAGGTGCAGGGGCCGATACTGGTGCTACCGGTTG[A/G]
GCCGATGGTGCATTGGGAGGAATCGGCTGGACAGCTGACTGATTATTAGTAATTAAGGGCCGATAATTTGGGAAAACACCTCCTGGTAAATAAACCGGTC

Reverse complement sequence

GACCGGTTTATTTACCAGGAGGTGTTTTCCCAAATTATCGGCCCTTAATTACTAATAATCAGTCAGCTGTCCAGCCGATTCCTCCCAATGCACCATCGGC[T/C]
CAACCGGTAGCACCAGTATCGGCCCCTGCACCTGCTGCACCATCATCGACACCGGGTCAATTAATTAATCCTCGGTTGTTGGTGAGAGAGCAACCACAGC

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 85.60% 0.00% 5.63% 8.72% NA
All Indica  2759 86.50% 0.00% 9.24% 4.20% NA
All Japonica  1512 80.70% 0.00% 0.60% 18.72% NA
Aus  269 98.90% 0.00% 0.74% 0.37% NA
Indica I  595 78.70% 0.00% 15.46% 5.88% NA
Indica II  465 93.30% 0.00% 4.09% 2.58% NA
Indica III  913 89.40% 0.10% 8.00% 2.52% NA
Indica Intermediate  786 85.10% 0.00% 9.03% 5.85% NA
Temperate Japonica  767 79.10% 0.00% 0.52% 20.34% NA
Tropical Japonica  504 83.70% 0.00% 0.40% 15.87% NA
Japonica Intermediate  241 79.30% 0.00% 1.24% 19.50% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 86.70% 0.00% 0.00% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1106565379 A -> DEL LOC_Os11g11820.1 N frameshift_variant Average:24.16; most accessible tissue: Zhenshan97 young leaf, score: 32.633 N N N N
vg1106565379 A -> G LOC_Os11g11820.1 synonymous_variant ; p.Ala164Ala; LOW synonymous_codon Average:24.16; most accessible tissue: Zhenshan97 young leaf, score: 32.633 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1106565379 NA 7.03E-06 mr1021 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
vg1106565379 NA 5.17E-06 mr1193 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
vg1106565379 NA 9.48E-09 mr1458 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
vg1106565379 NA 3.27E-06 mr1765 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
vg1106565379 2.25E-06 2.25E-06 mr1966 Ind_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