Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0122456656:

Variant ID: vg0122456656 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 22456656
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.80, T: 0.20, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


TTATCAAAAACATCACATCGAATCTTTAGACACATATATGGAACATTAAATATAGATAAAAAGAAAAACCAATTGCACAGTTTGTATGTAAATCGCGAGA[C/T]
GAATCTTTTGAGCCTAATTAGGCCATGATTAGCCATAAGTGCTACGGTAACCCACACGTGTTAATGACGAATTAATTAGGTTCAAAAGATTCGTCTCGCG

Reverse complement sequence

CGCGAGACGAATCTTTTGAACCTAATTAATTCGTCATTAACACGTGTGGGTTACCGTAGCACTTATGGCTAATCATGGCCTAATTAGGCTCAAAAGATTC[G/A]
TCTCGCGATTTACATACAAACTGTGCAATTGGTTTTTCTTTTTATCTATATTTAATGTTCCATATATGTGTCTAAAGATTCGATGTGATGTTTTTGATAA

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 48.80% 41.10% 1.59% 8.44% NA
All Indica  2759 32.40% 50.90% 2.46% 14.28% NA
All Japonica  1512 68.50% 31.30% 0.26% 0.00% NA
Aus  269 92.20% 7.80% 0.00% 0.00% NA
Indica I  595 6.40% 92.90% 0.34% 0.34% NA
Indica II  465 9.70% 55.70% 5.59% 29.03% NA
Indica III  913 56.50% 25.60% 1.64% 16.21% NA
Indica Intermediate  786 37.50% 45.40% 3.18% 13.87% NA
Temperate Japonica  767 96.20% 3.70% 0.13% 0.00% NA
Tropical Japonica  504 23.80% 75.80% 0.40% 0.00% NA
Japonica Intermediate  241 73.40% 26.10% 0.41% 0.00% NA
VI/Aromatic  96 92.70% 5.20% 0.00% 2.08% NA
Intermediate  90 46.70% 46.70% 3.33% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0122456656 C -> T LOC_Os01g39820.1 upstream_gene_variant ; 309.0bp to feature; MODIFIER silent_mutation Average:33.554; most accessible tissue: Zhenshan97 panicle, score: 85.254 N N N N
vg0122456656 C -> T LOC_Os01g39810.1 downstream_gene_variant ; 423.0bp to feature; MODIFIER silent_mutation Average:33.554; most accessible tissue: Zhenshan97 panicle, score: 85.254 N N N N
vg0122456656 C -> T LOC_Os01g39810.2 downstream_gene_variant ; 1099.0bp to feature; MODIFIER silent_mutation Average:33.554; most accessible tissue: Zhenshan97 panicle, score: 85.254 N N N N
vg0122456656 C -> T LOC_Os01g39810.4 downstream_gene_variant ; 1099.0bp to feature; MODIFIER silent_mutation Average:33.554; most accessible tissue: Zhenshan97 panicle, score: 85.254 N N N N
vg0122456656 C -> T LOC_Os01g39810.3 downstream_gene_variant ; 423.0bp to feature; MODIFIER silent_mutation Average:33.554; most accessible tissue: Zhenshan97 panicle, score: 85.254 N N N N
vg0122456656 C -> T LOC_Os01g39820-LOC_Os01g39830 intergenic_region ; MODIFIER silent_mutation Average:33.554; most accessible tissue: Zhenshan97 panicle, score: 85.254 N N N N
vg0122456656 C -> DEL N N silent_mutation Average:33.554; most accessible tissue: Zhenshan97 panicle, score: 85.254 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0122456656 NA 3.30E-07 mr1045 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
vg0122456656 NA 2.98E-09 mr1194 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
vg0122456656 NA 1.27E-07 mr1206 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
vg0122456656 NA 5.14E-06 mr1330 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
vg0122456656 NA 4.12E-07 mr1338 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
vg0122456656 NA 1.14E-09 mr1359 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
vg0122456656 NA 2.83E-08 mr1403 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
vg0122456656 NA 2.03E-06 mr1425 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
vg0122456656 NA 1.83E-06 mr1521 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
vg0122456656 NA 4.44E-06 mr1530 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
vg0122456656 NA 2.14E-06 mr1561 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
vg0122456656 NA 1.09E-06 mr1570 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
vg0122456656 NA 3.82E-07 mr1668 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
vg0122456656 NA 7.74E-07 mr1671 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
vg0122456656 NA 4.72E-08 mr1715 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
vg0122456656 NA 2.41E-07 mr1723 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
vg0122456656 NA 3.73E-06 mr1729 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
vg0122456656 NA 6.47E-06 mr1741 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
vg0122456656 NA 1.83E-06 mr1780 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
vg0122456656 NA 1.02E-07 mr1864 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
vg0122456656 NA 9.68E-06 mr1903 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
vg0122456656 NA 3.40E-06 mr1936 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
vg0122456656 NA 5.95E-06 mr1937 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
vg0122456656 NA 5.50E-07 mr1962 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
vg0122456656 NA 4.83E-07 mr1100_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
vg0122456656 NA 2.89E-06 mr1123_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
vg0122456656 NA 4.84E-10 mr1124_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
vg0122456656 NA 6.15E-06 mr1211_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
vg0122456656 NA 5.08E-07 mr1222_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
vg0122456656 NA 1.46E-06 mr1242_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
vg0122456656 NA 1.92E-07 mr1359_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
vg0122456656 NA 4.42E-07 mr1936_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