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Detailed information for vg0406137915:

Variant ID: vg0406137915 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 6137915
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCTCGTTGCGTGAAGCCTTTTGCCACAAGTCGCGCCTTAAACTTTTCTATATTCCCTCTGGAGTCATATTTGGTTTTAAAGACCCATTTACAGCCTACT[G/A]
TTTTGGCTCCTTTTGGGAATTTCTTCTAAATCCCAGAAATCGTTTAGTTTCATTGATTTCATTTCATCTTTCATGGTTTCCAACCATTCAGATGAGCGTG

Reverse complement sequence

CACGCTCATCTGAATGGTTGGAAACCATGAAAGATGAAATGAAATCAATGAAACTAAACGATTTCTGGGATTTAGAAGAAATTCCCAAAAGGAGCCAAAA[C/T]
AGTAGGCTGTAAATGGGTCTTTAAAACCAAATATGACTCCAGAGGGAATATAGAAAAGTTTAAGGCGCGACTTGTGGCAAAAGGCTTCACGCAACGAGAA

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 90.50% 2.70% 0.47% 6.35% NA
All Indica  2759 87.00% 3.10% 0.47% 9.46% NA
All Japonica  1512 94.80% 2.80% 0.53% 1.85% NA
Aus  269 97.80% 0.00% 0.37% 1.86% NA
Indica I  595 94.60% 0.00% 0.67% 4.71% NA
Indica II  465 75.10% 15.50% 0.86% 8.60% NA
Indica III  913 90.60% 0.20% 0.22% 8.98% NA
Indica Intermediate  786 84.10% 1.40% 0.38% 14.12% NA
Temperate Japonica  767 93.50% 5.50% 0.91% 0.13% NA
Tropical Japonica  504 95.00% 0.00% 0.20% 4.76% NA
Japonica Intermediate  241 98.30% 0.40% 0.00% 1.24% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 93.30% 1.10% 0.00% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0406137915 G -> DEL N N silent_mutation Average:14.955; most accessible tissue: Zhenshan97 flag leaf, score: 39.027 N N N N
vg0406137915 G -> A LOC_Os04g11240.1 upstream_gene_variant ; 3287.0bp to feature; MODIFIER silent_mutation Average:14.955; most accessible tissue: Zhenshan97 flag leaf, score: 39.027 N N N N
vg0406137915 G -> A LOC_Os04g11230.1 intron_variant ; MODIFIER silent_mutation Average:14.955; most accessible tissue: Zhenshan97 flag leaf, score: 39.027 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0406137915 1.05E-06 3.06E-08 mr1549_2 Jap_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
vg0406137915 8.09E-06 2.67E-07 mr1757_2 Jap_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