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Detailed information for vg1109788196:

Variant ID: vg1109788196 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 9788196
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCTCGTCACCGAAGACCTCTTTGATCATGTTAATGGCATGGCCCTTCAGCTCCCACTGGTCGTCGCACACTCGCTCGATCAGATACCAATACTTGAGCCT[C/G]
TCTCCGGCCATGGTCTCCGACCGGAGCACCAGGTCGGAGCTCATCTGCGGGTACGACGACTTGTCCCGGAGCAGCGCCCCGAGGTACGGCGGCACGGCGT

Reverse complement sequence

ACGCCGTGCCGCCGTACCTCGGGGCGCTGCTCCGGGACAAGTCGTCGTACCCGCAGATGAGCTCCGACCTGGTGCTCCGGTCGGAGACCATGGCCGGAGA[G/C]
AGGCTCAAGTATTGGTATCTGATCGAGCGAGTGTGCGACGACCAGTGGGAGCTGAAGGGCCATGCCATTAACATGATCAAAGAGGTCTTCGGTGACGAGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.20% 32.80% 0.02% 0.00% NA
All Indica  2759 98.80% 1.10% 0.04% 0.00% NA
All Japonica  1512 4.60% 95.40% 0.00% 0.00% NA
Aus  269 89.20% 10.80% 0.00% 0.00% NA
Indica I  595 98.70% 1.30% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 97.50% 2.40% 0.13% 0.00% NA
Temperate Japonica  767 3.50% 96.50% 0.00% 0.00% NA
Tropical Japonica  504 6.20% 93.80% 0.00% 0.00% NA
Japonica Intermediate  241 5.00% 95.00% 0.00% 0.00% NA
VI/Aromatic  96 81.20% 18.80% 0.00% 0.00% NA
Intermediate  90 68.90% 31.10% 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
vg1109788196 C -> G LOC_Os11g17580.1 missense_variant ; p.Glu173Asp; MODERATE nonsynonymous_codon ; E173D Average:72.807; most accessible tissue: Zhenshan97 young leaf, score: 87.584 unknown unknown TOLERATED 0.45

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1109788196 NA 1.64E-09 mr1005 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
vg1109788196 NA 2.71E-12 mr1449 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
vg1109788196 NA 3.22E-17 mr1566 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
vg1109788196 NA 2.12E-89 mr1758 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
vg1109788196 NA 1.06E-17 mr1767 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
vg1109788196 NA 5.48E-25 mr1484_2 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
vg1109788196 NA 2.91E-20 mr1900_2 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