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Detailed information for vg0325696417:

Variant ID: vg0325696417 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 25696417
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATAAAATTTCATTAAAAACTTTGCTTAATTCTATAATTCCTAGATTTTTCTGGGATTTATTTGAGCTAAGGAAGTATTTTTAATAAATGGAATTGCATTT[C/T]
ATGAATAATTTAAATTAGAAAAGGTTTTAAAAGTTCTCTTTTGGCTTTGGGCCGAAAGTCGGCCCAAAACCCTCTCTCTCTCTTCCTCGGCCCAGTCGGC

Reverse complement sequence

GCCGACTGGGCCGAGGAAGAGAGAGAGAGGGTTTTGGGCCGACTTTCGGCCCAAAGCCAAAAGAGAACTTTTAAAACCTTTTCTAATTTAAATTATTCAT[G/A]
AAATGCAATTCCATTTATTAAAAATACTTCCTTAGCTCAAATAAATCCCAGAAAAATCTAGGAATTATAGAATTAAGCAAAGTTTTTAATGAAATTTTAT

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 82.00% 2.20% 4.57% 11.28% NA
All Indica  2759 96.70% 0.00% 1.09% 2.14% NA
All Japonica  1512 59.20% 6.60% 8.66% 25.53% NA
Aus  269 75.80% 0.00% 7.81% 16.36% NA
Indica I  595 97.00% 0.00% 1.68% 1.34% NA
Indica II  465 97.80% 0.20% 1.51% 0.43% NA
Indica III  913 99.60% 0.00% 0.22% 0.22% NA
Indica Intermediate  786 92.60% 0.00% 1.40% 5.98% NA
Temperate Japonica  767 53.10% 10.30% 9.26% 27.38% NA
Tropical Japonica  504 73.60% 0.00% 6.35% 20.04% NA
Japonica Intermediate  241 48.50% 8.70% 11.62% 31.12% NA
VI/Aromatic  96 35.40% 0.00% 30.21% 34.38% NA
Intermediate  90 81.10% 1.10% 5.56% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0325696417 C -> T LOC_Os03g45519.1 upstream_gene_variant ; 2710.0bp to feature; MODIFIER silent_mutation Average:42.412; most accessible tissue: Minghui63 young leaf, score: 63.571 N N N N
vg0325696417 C -> T LOC_Os03g45528.1 upstream_gene_variant ; 1368.0bp to feature; MODIFIER silent_mutation Average:42.412; most accessible tissue: Minghui63 young leaf, score: 63.571 N N N N
vg0325696417 C -> T LOC_Os03g45550.1 upstream_gene_variant ; 3227.0bp to feature; MODIFIER silent_mutation Average:42.412; most accessible tissue: Minghui63 young leaf, score: 63.571 N N N N
vg0325696417 C -> T LOC_Os03g45540.1 downstream_gene_variant ; 456.0bp to feature; MODIFIER silent_mutation Average:42.412; most accessible tissue: Minghui63 young leaf, score: 63.571 N N N N
vg0325696417 C -> T LOC_Os03g45528-LOC_Os03g45540 intergenic_region ; MODIFIER silent_mutation Average:42.412; most accessible tissue: Minghui63 young leaf, score: 63.571 N N N N
vg0325696417 C -> DEL N N silent_mutation Average:42.412; most accessible tissue: Minghui63 young leaf, score: 63.571 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0325696417 8.13E-13 8.13E-13 mr1166 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
vg0325696417 8.09E-33 3.67E-39 mr1210 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
vg0325696417 3.09E-06 NA mr1252 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
vg0325696417 NA 9.31E-06 mr1280 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
vg0325696417 1.72E-32 6.66E-38 mr1305 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
vg0325696417 NA 3.34E-06 mr1358 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
vg0325696417 1.73E-10 1.23E-11 mr1379 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
vg0325696417 6.75E-18 6.76E-18 mr1409 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
vg0325696417 7.03E-10 1.57E-13 mr1515 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
vg0325696417 7.54E-13 4.52E-11 mr1559 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
vg0325696417 1.16E-33 2.66E-42 mr1585 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
vg0325696417 4.79E-36 3.26E-42 mr1586 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
vg0325696417 3.74E-10 3.74E-10 mr1649 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
vg0325696417 8.90E-07 8.90E-07 mr1703 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
vg0325696417 2.01E-19 5.22E-23 mr1765 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
vg0325696417 3.84E-06 1.77E-07 mr1793 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
vg0325696417 4.03E-09 4.03E-09 mr1166_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
vg0325696417 5.95E-33 5.28E-37 mr1305_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
vg0325696417 1.19E-10 2.14E-08 mr1379_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
vg0325696417 4.03E-14 8.53E-16 mr1409_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
vg0325696417 2.86E-14 8.05E-14 mr1559_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
vg0325696417 2.97E-40 3.15E-49 mr1585_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
vg0325696417 8.02E-08 8.02E-08 mr1649_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
vg0325696417 2.69E-11 4.29E-13 mr1703_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
vg0325696417 6.69E-08 8.00E-11 mr1765_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
vg0325696417 2.15E-09 5.93E-12 mr1793_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