Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0726230011:

Variant ID: vg0726230011 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 26230011
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTTGTTCTCATGACCGTAACGCATCGTCGCCTACTATTCGTTTTTTTCGTCTCCTTTTTTTTTGATTCGTTTTGTCGTGTTTTTTTGCTGTTTTTATC[C/T]
GGTTTCTTTTTCTTCATTGTTTGTTTTTTCCCGATTCGGTTTTTTTGCTAGGTCTCTTTTTCGCTTTTTTCACCCGGTTTTTTATCTCATCCGATCTGTT

Reverse complement sequence

AACAGATCGGATGAGATAAAAAACCGGGTGAAAAAAGCGAAAAAGAGACCTAGCAAAAAAACCGAATCGGGAAAAAACAAACAATGAAGAAAAAGAAACC[G/A]
GATAAAAACAGCAAAAAAACACGACAAAACGAATCAAAAAAAAAGGAGACGAAAAAAACGAATAGTAGGCGACGATGCGTTACGGTCATGAGAACAAAAA

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 56.60% 41.20% 1.82% 0.40% NA
All Indica  2759 90.20% 6.10% 3.04% 0.65% NA
All Japonica  1512 1.30% 98.60% 0.00% 0.07% NA
Aus  269 48.70% 51.30% 0.00% 0.00% NA
Indica I  595 85.90% 10.30% 3.03% 0.84% NA
Indica II  465 94.00% 4.10% 1.72% 0.22% NA
Indica III  913 93.60% 1.30% 4.27% 0.77% NA
Indica Intermediate  786 87.30% 9.70% 2.42% 0.64% NA
Temperate Japonica  767 1.20% 98.70% 0.00% 0.13% NA
Tropical Japonica  504 1.60% 98.40% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 34.40% 63.30% 2.22% 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
vg0726230011 C -> DEL N N silent_mutation Average:31.194; most accessible tissue: Callus, score: 59.223 N N N N
vg0726230011 C -> T LOC_Os07g43850.1 upstream_gene_variant ; 4588.0bp to feature; MODIFIER silent_mutation Average:31.194; most accessible tissue: Callus, score: 59.223 N N N N
vg0726230011 C -> T LOC_Os07g43870.1 upstream_gene_variant ; 660.0bp to feature; MODIFIER silent_mutation Average:31.194; most accessible tissue: Callus, score: 59.223 N N N N
vg0726230011 C -> T LOC_Os07g43870.2 upstream_gene_variant ; 668.0bp to feature; MODIFIER silent_mutation Average:31.194; most accessible tissue: Callus, score: 59.223 N N N N
vg0726230011 C -> T LOC_Os07g43870.3 upstream_gene_variant ; 668.0bp to feature; MODIFIER silent_mutation Average:31.194; most accessible tissue: Callus, score: 59.223 N N N N
vg0726230011 C -> T LOC_Os07g43860.1 downstream_gene_variant ; 3470.0bp to feature; MODIFIER silent_mutation Average:31.194; most accessible tissue: Callus, score: 59.223 N N N N
vg0726230011 C -> T LOC_Os07g43860-LOC_Os07g43870 intergenic_region ; MODIFIER silent_mutation Average:31.194; most accessible tissue: Callus, score: 59.223 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0726230011 NA 4.06E-09 mr1084_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
vg0726230011 NA 1.28E-14 mr1128_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
vg0726230011 NA 1.32E-15 mr1133_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
vg0726230011 NA 7.12E-09 mr1172_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
vg0726230011 NA 1.20E-09 mr1198_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
vg0726230011 NA 3.03E-08 mr1205_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
vg0726230011 NA 6.11E-07 mr1275_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
vg0726230011 NA 4.69E-21 mr1298_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
vg0726230011 NA 2.08E-07 mr1302_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
vg0726230011 NA 7.28E-06 mr1407_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
vg0726230011 NA 1.24E-06 mr1418_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
vg0726230011 NA 1.50E-06 mr1488_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
vg0726230011 NA 1.05E-09 mr1506_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
vg0726230011 NA 9.37E-16 mr1521_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
vg0726230011 NA 1.74E-15 mr1579_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
vg0726230011 NA 1.64E-07 mr1604_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
vg0726230011 NA 5.59E-12 mr1667_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
vg0726230011 4.50E-06 NA mr1667_2 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
vg0726230011 NA 8.79E-08 mr1681_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
vg0726230011 NA 8.70E-20 mr1731_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
vg0726230011 NA 4.16E-10 mr1751_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
vg0726230011 NA 4.34E-07 mr1824_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
vg0726230011 NA 1.70E-06 mr1834_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
vg0726230011 NA 2.74E-21 mr1924_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