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Detailed information for vg0406818237:

Variant ID: vg0406818237 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 6818237
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTACCTTGTACTTTTGCACCATTGTCCCCTTGCGGGTCTGCATAAATGAGTTTAAGAACTGGTTCCGTGCTTGCTGCATCATCGCTTCAAAATCTTTCTT[T/C]
TGATCGGGTGTCAGCTTGTCTGGAGTAATGTTCACGATGTTGCCTTCATTAACCTCGTATTGGTCTAACTGCTGGATCTTCACTTTAACAGAACCTGGGC

Reverse complement sequence

GCCCAGGTTCTGTTAAAGTGAAGATCCAGCAGTTAGACCAATACGAGGTTAATGAAGGCAACATCGTGAACATTACTCCAGACAAGCTGACACCCGATCA[A/G]
AAGAAAGATTTTGAAGCGATGATGCAGCAAGCACGGAACCAGTTCTTAAACTCATTTATGCAGACCCGCAAGGGGACAATGGTGCAAAAGTACAAGGTAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.10% 0.30% 7.53% 37.05% NA
All Indica  2759 36.40% 0.50% 10.87% 52.19% NA
All Japonica  1512 98.10% 0.00% 0.07% 1.85% NA
Aus  269 10.80% 0.00% 14.13% 75.09% NA
Indica I  595 40.30% 0.20% 11.26% 48.24% NA
Indica II  465 35.90% 0.90% 7.53% 55.70% NA
Indica III  913 32.00% 0.40% 13.36% 54.22% NA
Indica Intermediate  786 38.80% 0.80% 9.67% 50.76% NA
Temperate Japonica  767 99.90% 0.00% 0.00% 0.13% NA
Tropical Japonica  504 96.80% 0.00% 0.20% 2.98% NA
Japonica Intermediate  241 95.00% 0.00% 0.00% 4.98% NA
VI/Aromatic  96 27.10% 0.00% 15.62% 57.29% NA
Intermediate  90 67.80% 1.10% 2.22% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0406818237 T -> C LOC_Os04g12360.1 synonymous_variant ; p.Gln46Gln; LOW synonymous_codon Average:43.951; most accessible tissue: Minghui63 young leaf, score: 78.443 N N N N
vg0406818237 T -> DEL LOC_Os04g12360.1 N frameshift_variant Average:43.951; most accessible tissue: Minghui63 young leaf, score: 78.443 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0406818237 NA 1.64E-06 mr1015 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
vg0406818237 NA 4.14E-13 mr1035 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
vg0406818237 NA 1.17E-06 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
vg0406818237 NA 1.50E-06 mr1409 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
vg0406818237 NA 9.53E-06 mr1515 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
vg0406818237 NA 3.16E-12 mr1626 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
vg0406818237 NA 4.27E-06 mr1649 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
vg0406818237 1.95E-06 1.95E-06 mr1687 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
vg0406818237 NA 3.85E-06 mr1895 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
vg0406818237 NA 3.39E-07 mr1915 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
vg0406818237 5.17E-07 5.16E-07 mr1966 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
vg0406818237 4.02E-06 4.02E-06 mr1972 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
vg0406818237 NA 5.82E-18 mr1239_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
vg0406818237 NA 1.56E-16 mr1715_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