\

Search for Variation information by Variation ID:

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

Detailed information for vg0317967365:

Variant ID: vg0317967365 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 17967365
Reference Allele: GAlternative Allele: T,A
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTCAGCGTGAGCCGTCTCCCCAGCTAGGAACGCGTCTACTCCGTGGGAGACGTGGCTCTACGCTAGGAGCACCAGCTTTTCGCAGAGAGTCGGGCCTC[G/T,A]
CTCCTGCGAGGAGACCCGCTGCATGCTCCCGTCTCCTCGCCGCTCCCCCCAAATCCCCCTCCAATCCTCGCCCCCTCGCCTCTCTCCCACGGAGCTACCC

Reverse complement sequence

GGGTAGCTCCGTGGGAGAGAGGCGAGGGGGCGAGGATTGGAGGGGGATTTGGGGGGAGCGGCGAGGAGACGGGAGCATGCAGCGGGTCTCCTCGCAGGAG[C/A,T]
GAGGCCCGACTCTCTGCGAAAAGCTGGTGCTCCTAGCGTAGAGCCACGTCTCCCACGGAGTAGACGCGTTCCTAGCTGGGGAGACGGCTCACGCTGAAAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.80% 5.90% 0.02% 0.00% A: 0.21%
All Indica  2759 98.90% 1.10% 0.00% 0.00% NA
All Japonica  1512 99.20% 0.10% 0.07% 0.00% A: 0.66%
Aus  269 16.40% 83.60% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 98.70% 1.30% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 2.40% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 97.80% 0.00% 0.20% 0.00% A: 1.98%
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 78.10% 21.90% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0317967365 G -> T LOC_Os03g31540.1 missense_variant ; p.Ser333Arg; MODERATE nonsynonymous_codon ; S333R Average:70.929; most accessible tissue: Zhenshan97 young leaf, score: 87.004 unknown unknown DELETERIOUS 0.00
vg0317967365 G -> A LOC_Os03g31540.1 synonymous_variant ; p.Ser333Ser; LOW synonymous_codon Average:70.929; most accessible tissue: Zhenshan97 young leaf, score: 87.004 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0317967365 NA 7.63E-12 mr1471 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
vg0317967365 NA 2.12E-10 mr1499 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
vg0317967365 NA 7.47E-07 mr1530 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
vg0317967365 NA 2.57E-07 mr1706 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
vg0317967365 NA 5.60E-11 mr1722 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
vg0317967365 NA 1.72E-07 mr1735 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
vg0317967365 NA 5.17E-06 mr1952 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
vg0317967365 NA 2.26E-10 mr1047_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
vg0317967365 5.23E-06 NA mr1151_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
vg0317967365 2.11E-07 NA mr1248_2 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
vg0317967365 2.03E-07 NA mr1263_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
vg0317967365 NA 1.64E-21 mr1305_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
vg0317967365 NA 1.86E-12 mr1409_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
vg0317967365 NA 2.65E-15 mr1530_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
vg0317967365 NA 1.72E-06 mr1762_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
vg0317967365 NA 2.14E-06 mr1815_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
vg0317967365 2.82E-06 NA mr1835_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