\

Search for Variation information by Variation ID:

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

Detailed information for vg0317756145:

Variant ID: vg0317756145 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 17756145
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, T: 0.22, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


CAGTAAACATTTACTAATGGCGGATTAATTAGGCTTAATAAATCCGTCTCGTGGTTTACTGACGGATTCTGTAATTAGTTTTTTTATTAGTGCCCTAACA[C/T]
CCCATATGACACCCTATATAATACCCGATGTGACACGCCAAAACTTTACACTCCTGGATCTAAACACCCCCTAAGGTGTTGTTAAGATGTCTTGCTTTAT

Reverse complement sequence

ATAAAGCAAGACATCTTAACAACACCTTAGGGGGTGTTTAGATCCAGGAGTGTAAAGTTTTGGCGTGTCACATCGGGTATTATATAGGGTGTCATATGGG[G/A]
TGTTAGGGCACTAATAAAAAAACTAATTACAGAATCCGTCAGTAAACCACGAGACGGATTTATTAAGCCTAATTAATCCGCCATTAGTAAATGTTTACTG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.50% 33.20% 0.08% 0.21% NA
All Indica  2759 97.70% 2.00% 0.04% 0.22% NA
All Japonica  1512 8.30% 91.60% 0.00% 0.13% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 98.20% 1.70% 0.00% 0.17% NA
Indica II  465 96.80% 3.00% 0.00% 0.22% NA
Indica III  913 98.80% 1.10% 0.00% 0.11% NA
Indica Intermediate  786 96.70% 2.80% 0.13% 0.38% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 22.40% 77.20% 0.00% 0.40% NA
Japonica Intermediate  241 4.10% 95.90% 0.00% 0.00% NA
VI/Aromatic  96 13.50% 86.50% 0.00% 0.00% NA
Intermediate  90 50.00% 44.40% 3.33% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0317756145 C -> T LOC_Os03g31180.3 upstream_gene_variant ; 1684.0bp to feature; MODIFIER silent_mutation Average:55.782; most accessible tissue: Minghui63 flag leaf, score: 66.004 N N N N
vg0317756145 C -> T LOC_Os03g31180.1 intron_variant ; MODIFIER silent_mutation Average:55.782; most accessible tissue: Minghui63 flag leaf, score: 66.004 N N N N
vg0317756145 C -> T LOC_Os03g31180.2 intron_variant ; MODIFIER silent_mutation Average:55.782; most accessible tissue: Minghui63 flag leaf, score: 66.004 N N N N
vg0317756145 C -> DEL N N silent_mutation Average:55.782; most accessible tissue: Minghui63 flag leaf, score: 66.004 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0317756145 NA 2.77E-15 mr1323 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
vg0317756145 NA 1.25E-15 mr1376 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
vg0317756145 NA 5.52E-12 mr1386 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
vg0317756145 NA 1.25E-15 mr1431 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
vg0317756145 NA 1.42E-77 mr1718 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
vg0317756145 NA 2.07E-09 mr1718 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
vg0317756145 9.67E-08 6.69E-133 mr1750 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
vg0317756145 2.40E-10 9.86E-23 mr1750 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
vg0317756145 NA 2.19E-13 mr1924 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
vg0317756145 NA 6.00E-102 mr1987 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
vg0317756145 9.95E-10 9.94E-10 mr1987 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
vg0317756145 NA 5.76E-113 mr1718_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
vg0317756145 NA 2.19E-13 mr1718_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
vg0317756145 4.86E-07 7.26E-172 mr1750_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
vg0317756145 3.64E-12 1.15E-34 mr1750_2 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
vg0317756145 NA 2.86E-06 mr1896_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
vg0317756145 5.04E-10 1.26E-14 mr1987_2 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