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Detailed information for vg1117140650:

Variant ID: vg1117140650 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17140650
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACCAGGTGCACAAAGATTACAAGTGCTCTAGCCCCGAGTTATCTAAGTACCTCGCAGAAGTCGGGAAGCTAGAAAAAAGGTTGATGGGATCGAGGTCCG[G/A]
CACGTGTACTGCAAGGACAACATCGAACCTGACGACCTAGCACGGCGCGCGTCCAGACGAGAGCCACTCGAACCCGGCACCTTCCTGGACGTCTTGACAA

Reverse complement sequence

TTGTCAAGACGTCCAGGAAGGTGCCGGGTTCGAGTGGCTCTCGTCTGGACGCGCGCCGTGCTAGGTCGTCAGGTTCGATGTTGTCCTTGCAGTACACGTG[C/T]
CGGACCTCGATCCCATCAACCTTTTTTCTAGCTTCCCGACTTCTGCGAGGTACTTAGATAACTCGGGGCTAGAGCACTTGTAATCTTTGTGCACCTGGTT

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 70.00% 6.60% 7.66% 15.74% NA
All Indica  2759 79.00% 4.90% 7.10% 8.95% NA
All Japonica  1512 55.70% 8.90% 6.88% 28.57% NA
Aus  269 71.00% 0.70% 14.50% 13.75% NA
Indica I  595 82.20% 11.60% 3.19% 3.03% NA
Indica II  465 69.20% 0.00% 11.40% 19.35% NA
Indica III  913 81.20% 4.10% 6.35% 8.43% NA
Indica Intermediate  786 79.90% 3.80% 8.40% 7.89% NA
Temperate Japonica  767 89.40% 0.80% 0.52% 9.26% NA
Tropical Japonica  504 15.10% 20.80% 17.46% 46.63% NA
Japonica Intermediate  241 33.20% 9.50% 4.98% 52.28% NA
VI/Aromatic  96 35.40% 26.00% 16.67% 21.88% NA
Intermediate  90 67.80% 16.70% 7.78% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1117140650 G -> A LOC_Os11g29530.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:49.373; most accessible tissue: Zhenshan97 young leaf, score: 73.147 N N N N
vg1117140650 G -> A LOC_Os11g29550.1 upstream_gene_variant ; 4518.0bp to feature; MODIFIER silent_mutation Average:49.373; most accessible tissue: Zhenshan97 young leaf, score: 73.147 N N N N
vg1117140650 G -> A LOC_Os11g29540.1 downstream_gene_variant ; 2327.0bp to feature; MODIFIER silent_mutation Average:49.373; most accessible tissue: Zhenshan97 young leaf, score: 73.147 N N N N
vg1117140650 G -> DEL N N silent_mutation Average:49.373; most accessible tissue: Zhenshan97 young leaf, score: 73.147 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117140650 4.72E-06 4.72E-06 mr1703_2 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