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Detailed information for vg1105269968:

Variant ID: vg1105269968 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5269968
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGAGATAATTCTACTCGCTGGTTCTCGAACCAATAAATTGTAGCAATCTCTTAACTTCAGATGGTCGAGGTACGACTACGGCAATAGCGTAGCAGTCCTC[G/A]
CACCACGACTTCAGATGGTCGAGGTACGACTACGACTGGTCTTTGACCAGCAGCGTAGTGGTCCTCGCACCAAGACTTCAATCGGTCGAGAGATAAGGCT

Reverse complement sequence

AGCCTTATCTCTCGACCGATTGAAGTCTTGGTGCGAGGACCACTACGCTGCTGGTCAAAGACCAGTCGTAGTCGTACCTCGACCATCTGAAGTCGTGGTG[C/T]
GAGGACTGCTACGCTATTGCCGTAGTCGTACCTCGACCATCTGAAGTTAAGAGATTGCTACAATTTATTGGTTCGAGAACCAGCGAGTAGAATTATCTCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.30% 0.50% 1.44% 4.78% NA
All Indica  2759 99.10% 0.80% 0.04% 0.07% NA
All Japonica  1512 81.00% 0.00% 4.37% 14.68% NA
Aus  269 98.90% 0.00% 0.37% 0.74% NA
Indica I  595 99.00% 0.70% 0.17% 0.17% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 1.00% 0.00% 0.13% NA
Temperate Japonica  767 84.60% 0.00% 2.87% 12.52% NA
Tropical Japonica  504 83.50% 0.00% 2.98% 13.49% NA
Japonica Intermediate  241 63.90% 0.00% 12.03% 24.07% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg1105269968 G -> A LOC_Os11g09840-LOC_Os11g09850 intergenic_region ; MODIFIER silent_mutation Average:26.296; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N
vg1105269968 G -> DEL N N silent_mutation Average:26.296; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105269968 NA 1.38E-06 mr1516 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
vg1105269968 NA 3.66E-06 mr1544 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
vg1105269968 NA 8.75E-06 mr1569 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
vg1105269968 8.70E-06 NA mr1599 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
vg1105269968 NA 1.91E-07 mr1881 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
vg1105269968 NA 8.91E-07 mr1960 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