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Detailed information for vg1109851703:

Variant ID: vg1109851703 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 9851703
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGGTTCGATACTTGGCGAAACCCATGCCCTTCGTGGGCTTTCGCCTCGCGGACTTCAACCGTACGACCCTCCGGCAGAGTCCATCTTTGGCGAAGCTTGT[C/T]
AGCTCGATACCACGGCTTTCGCTTATGTTCTCCCTTCGACCGTCGCTGCTTGCCTCCGGCTCATGCCTTTGCTTATGTCCTTCGTTTCGGTAGGCCCGGC

Reverse complement sequence

GCCGGGCCTACCGAAACGAAGGACATAAGCAAAGGCATGAGCCGGAGGCAAGCAGCGACGGTCGAAGGGAGAACATAAGCGAAAGCCGTGGTATCGAGCT[G/A]
ACAAGCTTCGCCAAAGATGGACTCTGCCGGAGGGTCGTACGGTTGAAGTCCGCGAGGCGAAAGCCCACGAAGGGCATGGGTTTCGCCAAGTATCGAACCT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.70% 19.30% 0.00% 0.00% NA
All Indica  2759 68.40% 31.60% 0.00% 0.00% NA
All Japonica  1512 99.40% 0.60% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 90.40% 9.60% 0.00% 0.00% NA
Indica II  465 20.00% 80.00% 0.00% 0.00% NA
Indica III  913 79.10% 20.90% 0.00% 0.00% NA
Indica Intermediate  786 67.80% 32.20% 0.00% 0.00% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 70.00% 30.00% 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
vg1109851703 C -> T LOC_Os11g17650.1 synonymous_variant ; p.Leu62Leu; LOW synonymous_codon Average:65.023; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1109851703 NA 1.90E-07 mr1557 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
vg1109851703 NA 3.25E-09 mr1557_2 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
vg1109851703 NA 7.71E-15 mr1598_2 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
vg1109851703 NA 5.10E-07 mr1805_2 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