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Detailed information for vg0406035761:

Variant ID: vg0406035761 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 6035761
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCTGTGAAATCGACACACATGCGCCATTTGCCGTTTGACTTCCGCACCAGCACTGGATTCGCCAACCACTCCGTATGGTCAATCTCTTGGATAACCCCC[G/A]
CCCGGAGTAATTTTTGTACTTCGGCCTTCGCCGTTTCTTGGCGAACGCAGACATCTTGCGCAACTTTTGTTTTCTTGGCTTAATATCCGGCTTGACTGCT

Reverse complement sequence

AGCAGTCAAGCCGGATATTAAGCCAAGAAAACAAAAGTTGCGCAAGATGTCTGCGTTCGCCAAGAAACGGCGAAGGCCGAAGTACAAAAATTACTCCGGG[C/T]
GGGGGTTATCCAAGAGATTGACCATACGGAGTGGTTGGCGAATCCAGTGCTGGTGCGGAAGTCAAACGGCAAATGGCGCATGTGTGTCGATTTCACAGAT

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 94.30% 5.40% 0.34% 0.00% NA
All Indica  2759 90.50% 9.00% 0.58% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 94.60% 5.00% 0.34% 0.00% NA
Indica II  465 95.10% 2.60% 2.37% 0.00% NA
Indica III  913 86.50% 13.30% 0.22% 0.00% NA
Indica Intermediate  786 89.20% 10.70% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0406035761 G -> A LOC_Os04g11080.1 downstream_gene_variant ; 4353.0bp to feature; MODIFIER silent_mutation Average:32.986; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 N N N N
vg0406035761 G -> A LOC_Os04g11090.1 intron_variant ; MODIFIER silent_mutation Average:32.986; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0406035761 NA 4.36E-06 mr1246 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
vg0406035761 NA 4.45E-08 mr1305 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
vg0406035761 NA 1.51E-09 mr1586 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
vg0406035761 NA 3.83E-07 mr1765 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