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Detailed information for vg0804463783:

Variant ID: vg0804463783 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 4463783
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGAAATCATCGAAATTTCAATCAATAACTATAAATAGAGGTAAACTAAAATTGTTTTCCTTTTTTAATTCGTTATTCTTTTCTTTCCTATTGTAAATTT[C/T]
AGTAAATACATGGAATACATCAGTTTTTTTGAAAATTTATATCCCAATAGGTTCTATGAATATCATACTATTTATAAGATTTTATTTGATTTTTTCCTTT

Reverse complement sequence

AAAGGAAAAAATCAAATAAAATCTTATAAATAGTATGATATTCATAGAACCTATTGGGATATAAATTTTCAAAAAAACTGATGTATTCCATGTATTTACT[G/A]
AAATTTACAATAGGAAAGAAAAGAATAACGAATTAAAAAAGGAAAACAATTTTAGTTTACCTCTATTTATAGTTATTGATTGAAATTTCGATGATTTCGC

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 38.20% 0.10% 0.55% 61.09% NA
All Indica  2759 10.10% 0.10% 0.76% 88.98% NA
All Japonica  1512 95.20% 0.00% 0.07% 4.76% NA
Aus  269 9.70% 0.40% 1.49% 88.48% NA
Indica I  595 16.60% 0.00% 1.18% 82.18% NA
Indica II  465 11.80% 0.00% 0.65% 87.53% NA
Indica III  913 2.80% 0.10% 0.33% 96.71% NA
Indica Intermediate  786 12.70% 0.30% 1.02% 86.01% NA
Temperate Japonica  767 98.30% 0.00% 0.13% 1.56% NA
Tropical Japonica  504 89.10% 0.00% 0.00% 10.91% NA
Japonica Intermediate  241 97.90% 0.00% 0.00% 2.07% NA
VI/Aromatic  96 24.00% 0.00% 0.00% 76.04% NA
Intermediate  90 43.30% 2.20% 0.00% 54.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0804463783 C -> T LOC_Os08g07900.1 upstream_gene_variant ; 3560.0bp to feature; MODIFIER silent_mutation Average:14.69; most accessible tissue: Callus, score: 29.336 N N N N
vg0804463783 C -> T LOC_Os08g07910.1 upstream_gene_variant ; 2662.0bp to feature; MODIFIER silent_mutation Average:14.69; most accessible tissue: Callus, score: 29.336 N N N N
vg0804463783 C -> T LOC_Os08g07930.1 upstream_gene_variant ; 2246.0bp to feature; MODIFIER silent_mutation Average:14.69; most accessible tissue: Callus, score: 29.336 N N N N
vg0804463783 C -> T LOC_Os08g07920.1 intron_variant ; MODIFIER silent_mutation Average:14.69; most accessible tissue: Callus, score: 29.336 N N N N
vg0804463783 C -> DEL N N silent_mutation Average:14.69; most accessible tissue: Callus, score: 29.336 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0804463783 NA 3.52E-07 mr1004 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
vg0804463783 NA 1.82E-07 mr1006 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
vg0804463783 NA 9.47E-08 mr1052 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
vg0804463783 NA 1.77E-15 mr1158 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
vg0804463783 NA 6.05E-06 mr1209 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
vg0804463783 NA 2.58E-07 mr1230 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
vg0804463783 NA 1.53E-06 mr1321 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
vg0804463783 NA 8.78E-09 mr1348 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
vg0804463783 NA 9.34E-06 mr1349 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
vg0804463783 NA 2.39E-06 mr1365 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
vg0804463783 NA 2.51E-06 mr1545 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
vg0804463783 NA 5.70E-08 mr1621 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
vg0804463783 NA 4.75E-06 mr1665 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
vg0804463783 NA 1.75E-09 mr1939 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