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Detailed information for vg0807735012:

Variant ID: vg0807735012 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 7735012
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.79, T: 0.21, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTTCTCCATGTCAAATTGAATTGGATCTCTGATTCTTTTGTGCATTGGCCAGCGTATGTGATGAACTCATACGGATACGGACACAATCAGGGACGACG[C/T]
ACGAAATTTGTGGCAAAAACATGTTAAACTTTTATAATAGGAAAAGAAGTAGAGAAGAGATAGAGAGAAATAGAGATGGGCACGCTATAAATAAAACTAT

Reverse complement sequence

ATAGTTTTATTTATAGCGTGCCCATCTCTATTTCTCTCTATCTCTTCTCTACTTCTTTTCCTATTATAAAAGTTTAACATGTTTTTGCCACAAATTTCGT[G/A]
CGTCGTCCCTGATTGTGTCCGTATCCGTATGAGTTCATCACATACGCTGGCCAATGCACAAAAGAATCAGAGATCCAATTCAATTTGACATGGAGAAAAA

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 32.80% 15.30% 0.66% 51.25% NA
All Indica  2759 2.80% 18.40% 0.98% 77.85% NA
All Japonica  1512 95.00% 2.20% 0.00% 2.78% NA
Aus  269 0.00% 58.00% 0.74% 41.26% NA
Indica I  595 2.50% 7.60% 0.34% 89.58% NA
Indica II  465 4.30% 26.90% 2.15% 66.67% NA
Indica III  913 2.00% 19.80% 0.55% 77.66% NA
Indica Intermediate  786 3.10% 19.80% 1.27% 75.83% NA
Temperate Japonica  767 97.50% 1.00% 0.00% 1.43% NA
Tropical Japonica  504 93.30% 2.80% 0.00% 3.97% NA
Japonica Intermediate  241 90.50% 5.00% 0.00% 4.56% NA
VI/Aromatic  96 3.10% 12.50% 0.00% 84.38% NA
Intermediate  90 38.90% 14.40% 2.22% 44.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0807735012 C -> T LOC_Os08g13020.1 upstream_gene_variant ; 480.0bp to feature; MODIFIER silent_mutation Average:24.154; most accessible tissue: Callus, score: 56.379 N N N N
vg0807735012 C -> T LOC_Os08g13014.1 downstream_gene_variant ; 2310.0bp to feature; MODIFIER silent_mutation Average:24.154; most accessible tissue: Callus, score: 56.379 N N N N
vg0807735012 C -> T LOC_Os08g13014-LOC_Os08g13020 intergenic_region ; MODIFIER silent_mutation Average:24.154; most accessible tissue: Callus, score: 56.379 N N N N
vg0807735012 C -> DEL N N silent_mutation Average:24.154; most accessible tissue: Callus, score: 56.379 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0807735012 NA 1.29E-21 mr1168 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
vg0807735012 NA 2.39E-46 mr1194 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
vg0807735012 1.90E-06 1.23E-06 mr1268 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
vg0807735012 NA 1.28E-23 mr1383 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
vg0807735012 NA 4.16E-22 mr1548 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
vg0807735012 NA 4.55E-22 mr1588 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
vg0807735012 NA 1.25E-09 mr1714 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
vg0807735012 NA 1.45E-18 mr1715 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
vg0807735012 NA 7.95E-24 mr1917 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
vg0807735012 NA 2.67E-06 mr1991 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
vg0807735012 NA 1.27E-08 mr1004_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
vg0807735012 NA 1.05E-19 mr1168_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
vg0807735012 NA 2.89E-19 mr1383_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
vg0807735012 NA 9.14E-27 mr1588_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
vg0807735012 NA 1.07E-07 mr1588_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
vg0807735012 NA 2.91E-16 mr1715_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
vg0807735012 NA 8.43E-11 mr1893_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