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Detailed information for vg1109788700:

Variant ID: vg1109788700 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 9788700
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGTCTCCTTGAGCTCCTTCAGCGACTTCTCGGTGAGGTAATTGTGGCCACTGTTGCCGCCGGTGAGGGTCAGCTTGAAGATGTCATCCTTCTCTTTGTA[A/G]
GTGCAGAAGCCCATGACGATGTTCAGTGGGGGACGAGTAGTAGCTAGGAAGTATTCTTCAACTCTCACCCAAGGTCTGCACCACTATTTAAAGGACAGCT

Reverse complement sequence

AGCTGTCCTTTAAATAGTGGTGCAGACCTTGGGTGAGAGTTGAAGAATACTTCCTAGCTACTACTCGTCCCCCACTGAACATCGTCATGGGCTTCTGCAC[T/C]
TACAAAGAGAAGGATGACATCTTCAAGCTGACCCTCACCGGCGGCAACAGTGGCCACAATTACCTCACCGAGAAGTCGCTGAAGGAGCTCAAGGAGACGC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.10% 5.90% 0.00% 0.00% NA
All Indica  2759 93.00% 7.00% 0.00% 0.00% NA
All Japonica  1512 98.90% 1.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.80% 3.20% 0.00% 0.00% NA
Indica II  465 96.10% 3.90% 0.00% 0.00% NA
Indica III  913 96.50% 3.50% 0.00% 0.00% NA
Indica Intermediate  786 84.10% 15.90% 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 96.70% 3.30% 0.00% 0.00% NA
VI/Aromatic  96 31.20% 68.80% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg1109788700 A -> G LOC_Os11g17580.1 synonymous_variant ; p.Thr5Thr; LOW synonymous_codon Average:80.308; most accessible tissue: Callus, score: 89.32 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1109788700 NA 4.11E-06 mr1100 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
vg1109788700 NA 6.84E-07 mr1723_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