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

Detailed information for vg0726050168:

Variant ID: vg0726050168 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 26050168
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTAACTCCTCCGCCGCCGCTCGCCGTCGCCGGAGATCCCTATCTCCCTCCCCTCCTCGGCCGCAACCACTTTCCCCCTCCATCGCCGCCACAATCGCCA[A/G]
CCCTAGCACCGCCAGCTTGAATTGGGGAACGACTGGAGGTTGAAGAAGAGAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGACTGACAGGTGGGAC

Reverse complement sequence

GTCCCACCTGTCAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTCTCTTCTTCAACCTCCAGTCGTTCCCCAATTCAAGCTGGCGGTGCTAGGG[T/C]
TGGCGATTGTGGCGGCGATGGAGGGGGAAAGTGGTTGCGGCCGAGGAGGGGAGGGAGATAGGGATCTCCGGCGACGGCGAGCGGCGGCGGAGGAGTTAAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.20% 8.30% 5.50% 1.04% NA
All Indica  2759 75.20% 13.90% 9.13% 1.70% NA
All Japonica  1512 99.60% 0.10% 0.26% 0.00% NA
Aus  269 97.40% 0.70% 1.49% 0.37% NA
Indica I  595 58.80% 24.90% 15.63% 0.67% NA
Indica II  465 88.80% 4.90% 5.38% 0.86% NA
Indica III  913 78.40% 11.70% 6.46% 3.40% NA
Indica Intermediate  786 76.00% 13.50% 9.54% 1.02% NA
Temperate Japonica  767 99.70% 0.00% 0.26% 0.00% NA
Tropical Japonica  504 99.20% 0.40% 0.40% 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% 2.20% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0726050168 A -> DEL N N silent_mutation Average:57.21; most accessible tissue: Minghui63 young leaf, score: 78.054 N N N N
vg0726050168 A -> G LOC_Os07g43540.1 upstream_gene_variant ; 2676.0bp to feature; MODIFIER silent_mutation Average:57.21; most accessible tissue: Minghui63 young leaf, score: 78.054 N N N N
vg0726050168 A -> G LOC_Os07g43560.1 downstream_gene_variant ; 2054.0bp to feature; MODIFIER silent_mutation Average:57.21; most accessible tissue: Minghui63 young leaf, score: 78.054 N N N N
vg0726050168 A -> G LOC_Os07g43540-LOC_Os07g43560 intergenic_region ; MODIFIER silent_mutation Average:57.21; most accessible tissue: Minghui63 young leaf, score: 78.054 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0726050168 NA 6.81E-06 mr1074 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
vg0726050168 NA 7.41E-07 mr1170 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
vg0726050168 9.54E-06 1.06E-06 mr1185 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
vg0726050168 NA 5.93E-07 mr1189 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
vg0726050168 NA 5.64E-07 mr1215 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
vg0726050168 NA 1.17E-06 mr1245 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
vg0726050168 NA 3.34E-07 mr1269 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
vg0726050168 6.02E-07 2.64E-08 mr1425 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
vg0726050168 1.95E-06 1.43E-06 mr1425 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
vg0726050168 NA 5.58E-06 mr1450 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
vg0726050168 NA 2.46E-06 mr1461 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
vg0726050168 NA 7.35E-06 mr1502 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
vg0726050168 NA 9.37E-07 mr1511 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
vg0726050168 NA 1.71E-07 mr1625 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
vg0726050168 9.11E-06 8.87E-07 mr1625 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
vg0726050168 NA 9.87E-06 mr1654 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
vg0726050168 NA 3.03E-06 mr1683 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
vg0726050168 NA 4.03E-06 mr1734 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
vg0726050168 NA 7.27E-06 mr1782 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
vg0726050168 NA 1.01E-06 mr1796 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
vg0726050168 NA 2.11E-06 mr1975 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
vg0726050168 NA 2.63E-07 mr1805_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