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Detailed information for vg0207676313:

Variant ID: vg0207676313 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 7676313
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTAAATTTTATAAAACTACAGTACTTTGATCGAAGTATTATAAAAGTACAGATTTAAGGCGTCGTATTATAAAACTACATATTTAACACAAAATTTATCA[C/T]
AAAACTATAGATTTAATACTAGAGTATCACAAAACTACATATTTTACAGCTTAAATTCCTACCACTACTGCTATGTTAGAGTGATAAATGTGTAGTTTTG

Reverse complement sequence

CAAAACTACACATTTATCACTCTAACATAGCAGTAGTGGTAGGAATTTAAGCTGTAAAATATGTAGTTTTGTGATACTCTAGTATTAAATCTATAGTTTT[G/A]
TGATAAATTTTGTGTTAAATATGTAGTTTTATAATACGACGCCTTAAATCTGTACTTTTATAATACTTCGATCAAAGTACTGTAGTTTTATAAAATTTAC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.10% 12.70% 0.30% 0.00% NA
All Indica  2759 90.10% 9.80% 0.14% 0.00% NA
All Japonica  1512 79.20% 20.10% 0.66% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 96.60% 3.20% 0.22% 0.00% NA
Indica III  913 80.80% 19.10% 0.11% 0.00% NA
Indica Intermediate  786 90.20% 9.50% 0.25% 0.00% NA
Temperate Japonica  767 94.10% 4.70% 1.17% 0.00% NA
Tropical Japonica  504 62.70% 37.30% 0.00% 0.00% NA
Japonica Intermediate  241 66.40% 33.20% 0.41% 0.00% NA
VI/Aromatic  96 84.40% 15.60% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 0.00% 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
vg0207676313 C -> T LOC_Os02g14040.1 upstream_gene_variant ; 3549.0bp to feature; MODIFIER silent_mutation Average:41.509; most accessible tissue: Callus, score: 61.536 N N N N
vg0207676313 C -> T LOC_Os02g14059.1 upstream_gene_variant ; 498.0bp to feature; MODIFIER silent_mutation Average:41.509; most accessible tissue: Callus, score: 61.536 N N N N
vg0207676313 C -> T LOC_Os02g14059.2 upstream_gene_variant ; 498.0bp to feature; MODIFIER silent_mutation Average:41.509; most accessible tissue: Callus, score: 61.536 N N N N
vg0207676313 C -> T LOC_Os02g14040-LOC_Os02g14059 intergenic_region ; MODIFIER silent_mutation Average:41.509; most accessible tissue: Callus, score: 61.536 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0207676313 9.76E-06 NA mr1035_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
vg0207676313 9.38E-06 NA mr1137_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
vg0207676313 8.05E-07 8.05E-07 mr1147_2 Jap_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
vg0207676313 NA 1.50E-06 mr1149_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
vg0207676313 NA 9.79E-06 mr1204_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
vg0207676313 6.29E-06 6.29E-06 mr1279_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
vg0207676313 5.64E-07 5.64E-07 mr1313_2 Jap_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
vg0207676313 NA 2.14E-06 mr1369_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
vg0207676313 NA 5.88E-07 mr1441_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
vg0207676313 NA 4.46E-07 mr1453_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
vg0207676313 NA 3.48E-06 mr1467_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
vg0207676313 NA 5.83E-06 mr1467_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
vg0207676313 2.60E-07 2.60E-07 mr1473_2 Jap_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
vg0207676313 NA 7.40E-06 mr1556_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
vg0207676313 NA 3.10E-06 mr1596_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
vg0207676313 NA 4.94E-06 mr1596_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
vg0207676313 2.11E-07 2.11E-07 mr1630_2 Jap_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
vg0207676313 5.05E-06 5.06E-06 mr1703_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
vg0207676313 NA 4.67E-06 mr1764_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
vg0207676313 1.32E-06 1.32E-06 mr1777_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
vg0207676313 2.40E-06 2.40E-06 mr1777_2 Jap_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
vg0207676313 NA 6.90E-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
vg0207676313 6.07E-06 6.07E-06 mr1985_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