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Detailed information for vg0708765167:

Variant ID: vg0708765167 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 8765167
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACTGCCAGGATGAATGGCATACTGAGTTTGATGAGCTTCTGTCAGTATCAAGTCCTTTAACTTTAACTCTTTGTTTTCAGGTACACACAATCTTTCTCC[T/C]
ATCCAGATTGTTCCTTGTTCATCCTCAACAAAACCTCGGGCTTTTCCAACTCTCATGTTCTTTTTGAGCTCTCTATTTCAGGATCACTTGCTTGAGCTAT

Reverse complement sequence

ATAGCTCAAGCAAGTGATCCTGAAATAGAGAGCTCAAAAAGAACATGAGAGTTGGAAAAGCCCGAGGTTTTGTTGAGGATGAACAAGGAACAATCTGGAT[A/G]
GGAGAAAGATTGTGTGTACCTGAAAACAAAGAGTTAAAGTTAAAGGACTTGATACTGACAGAAGCTCATCAAACTCAGTATGCCATTCATCCTGGCAGTA

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 39.40% 6.70% 3.39% 50.57% NA
All Indica  2759 7.50% 4.50% 3.81% 84.16% NA
All Japonica  1512 89.30% 6.20% 3.17% 1.32% NA
Aus  269 61.70% 33.50% 0.74% 4.09% NA
Indica I  595 5.40% 0.20% 4.87% 89.58% NA
Indica II  465 9.70% 0.20% 1.29% 88.82% NA
Indica III  913 6.40% 7.30% 2.19% 84.12% NA
Indica Intermediate  786 9.30% 7.00% 6.36% 77.35% NA
Temperate Japonica  767 87.40% 11.70% 0.13% 0.78% NA
Tropical Japonica  504 89.10% 0.00% 8.93% 1.98% NA
Japonica Intermediate  241 95.90% 1.70% 0.83% 1.66% NA
VI/Aromatic  96 89.60% 2.10% 2.08% 6.25% NA
Intermediate  90 56.70% 5.60% 3.33% 34.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0708765167 T -> DEL N N silent_mutation Average:9.834; most accessible tissue: Callus, score: 22.566 N N N N
vg0708765167 T -> C LOC_Os07g15200.1 upstream_gene_variant ; 3556.0bp to feature; MODIFIER silent_mutation Average:9.834; most accessible tissue: Callus, score: 22.566 N N N N
vg0708765167 T -> C LOC_Os07g15210.1 intron_variant ; MODIFIER silent_mutation Average:9.834; most accessible tissue: Callus, score: 22.566 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0708765167 NA 5.01E-06 mr1053_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
vg0708765167 NA 2.08E-12 mr1147_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
vg0708765167 NA 1.33E-07 mr1149_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
vg0708765167 NA 2.32E-06 mr1161_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
vg0708765167 NA 4.18E-06 mr1264_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
vg0708765167 NA 3.41E-06 mr1270_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
vg0708765167 NA 1.85E-24 mr1316_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
vg0708765167 NA 3.26E-09 mr1379_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
vg0708765167 NA 3.27E-08 mr1408_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
vg0708765167 NA 1.79E-22 mr1551_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
vg0708765167 NA 3.94E-13 mr1552_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
vg0708765167 NA 3.05E-06 mr1559_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
vg0708765167 NA 2.93E-06 mr1592_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
vg0708765167 NA 7.76E-15 mr1720_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
vg0708765167 NA 2.83E-07 mr1804_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