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Detailed information for vg1127979682:

Variant ID: vg1127979682 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27979682
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTGTATCTCCTGTGGGAGCTTAGTGATTCGCGTACCCTTGAGACCTAGGTACTTGAGCAGCCTGAGGCTCTCTAGCTGCTCACATATCTTCTTCAGGTG[G/A]
GAGTCCTCTATACCGATATTATCTTCAAGGTCCAACACTCGCAATCTTTTAAACATATCCAAGGGGACTCCTATCACGTCGCCAAGGATGACAAGGCTGC

Reverse complement sequence

GCAGCCTTGTCATCCTTGGCGACGTGATAGGAGTCCCCTTGGATATGTTTAAAAGATTGCGAGTGTTGGACCTTGAAGATAATATCGGTATAGAGGACTC[C/T]
CACCTGAAGAAGATATGTGAGCAGCTAGAGAGCCTCAGGCTGCTCAAGTACCTAGGTCTCAAGGGTACGCGAATCACTAAGCTCCCACAGGAGATACAGA

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 42.80% 16.00% 1.12% 40.03% NA
All Indica  2759 42.80% 20.40% 0.83% 35.92% NA
All Japonica  1512 41.30% 10.40% 1.72% 46.63% NA
Aus  269 58.70% 1.50% 1.12% 38.66% NA
Indica I  595 17.50% 41.00% 1.01% 40.50% NA
Indica II  465 46.20% 1.50% 1.72% 50.54% NA
Indica III  913 52.90% 21.40% 0.33% 25.41% NA
Indica Intermediate  786 48.30% 14.90% 0.76% 36.01% NA
Temperate Japonica  767 29.90% 15.80% 2.35% 52.02% NA
Tropical Japonica  504 55.80% 5.00% 1.19% 38.10% NA
Japonica Intermediate  241 47.30% 4.60% 0.83% 47.30% NA
VI/Aromatic  96 12.50% 25.00% 0.00% 62.50% NA
Intermediate  90 54.40% 8.90% 1.11% 35.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1127979682 G -> A LOC_Os11g46200.1 synonymous_variant ; p.Ser688Ser; LOW synonymous_codon Average:43.882; most accessible tissue: Callus, score: 81.053 N N N N
vg1127979682 G -> A LOC_Os11g46200.1 synonymous_variant ; p.Ser688Ser; LOW nonsynonymous_codon ; S688F Average:43.882; most accessible tissue: Callus, score: 81.053 possibly damaging 1.806 DELETERIOUS 0.01
vg1127979682 G -> DEL LOC_Os11g46200.1 N frameshift_variant Average:43.882; most accessible tissue: Callus, score: 81.053 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127979682 NA 6.28E-06 mr1555 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
vg1127979682 NA 3.35E-06 mr1609 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