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Detailed information for vg0406877172:

Variant ID: vg0406877172 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 6877172
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.95, G: 0.06, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


ATGATGATTTTAAGTGCACAAGCTACCCTAATCTGTTCAGTGTGACTTTGTATAAGAATGATTCAGTTAGGACCATGTGCCTACGGCCAATGGAGGACTC[T/G]
TTTGTTCTTCCCCTCTCAGATGATGCATGTGGAGAATTTTTGCAACTGCAAGAGGAATTGAATCATCTGCAGCTTCAGCTAGGAAGAAGTGATGTTTGGA

Reverse complement sequence

TCCAAACATCACTTCTTCCTAGCTGAAGCTGCAGATGATTCAATTCCTCTTGCAGTTGCAAAAATTCTCCACATGCATCATCTGAGAGGGGAAGAACAAA[A/C]
GAGTCCTCCATTGGCCGTAGGCACATGGTCCTAACTGAATCATTCTTATACAAAGTCACACTGAACAGATTAGGGTAGCTTGTGCACTTAAAATCATCAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 49.60% 37.00% 4.51% 8.87% NA
All Indica  2759 27.30% 55.10% 6.09% 11.60% NA
All Japonica  1512 99.30% 0.30% 0.33% 0.13% NA
Aus  269 3.00% 69.50% 0.37% 27.14% NA
Indica I  595 10.90% 70.30% 8.07% 10.76% NA
Indica II  465 23.00% 60.60% 9.25% 7.10% NA
Indica III  913 38.00% 42.90% 4.38% 14.68% NA
Indica Intermediate  786 29.60% 54.30% 4.71% 11.32% NA
Temperate Japonica  767 99.70% 0.10% 0.00% 0.13% NA
Tropical Japonica  504 99.40% 0.40% 0.00% 0.20% NA
Japonica Intermediate  241 97.50% 0.40% 2.07% 0.00% NA
VI/Aromatic  96 31.20% 17.70% 34.38% 16.67% NA
Intermediate  90 58.90% 25.60% 6.67% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0406877172 T -> DEL LOC_Os04g12440.1 N frameshift_variant Average:33.327; most accessible tissue: Minghui63 flower, score: 60.203 N N N N
vg0406877172 T -> G LOC_Os04g12440.1 synonymous_variant ; p.Ser651Ser; LOW synonymous_codon Average:33.327; most accessible tissue: Minghui63 flower, score: 60.203 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0406877172 NA 6.94E-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
vg0406877172 NA 2.46E-07 mr1133 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
vg0406877172 NA 7.59E-06 mr1613 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
vg0406877172 6.40E-06 6.40E-06 mr1777 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
vg0406877172 NA 3.74E-06 mr1798 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
vg0406877172 NA 3.22E-06 mr1846 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
vg0406877172 NA 3.76E-08 mr1004_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
vg0406877172 NA 1.38E-06 mr1062_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
vg0406877172 3.05E-06 NA mr1882_2 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
vg0406877172 NA 6.00E-07 mr1882_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