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Detailed information for vg0221843984:

Variant ID: vg0221843984 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 21843984
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTTCCCAAAAACATCACATCGAATCTTTGAATATATGTATGAAGCATTAAATATAGATAAAGTGAAAAACTAACTGCACAGTTTGGAAATCGCGAGAC[G/T]
AATCTTTTGTGCCTAATTAGTCTATGATTAGCCATAAGTGCTACATGCAACCCACATACGCTAATAATGGATTAATTAGGCTTAATAAATTCGTCTCGTG

Reverse complement sequence

CACGAGACGAATTTATTAAGCCTAATTAATCCATTATTAGCGTATGTGGGTTGCATGTAGCACTTATGGCTAATCATAGACTAATTAGGCACAAAAGATT[C/A]
GTCTCGCGATTTCCAAACTGTGCAGTTAGTTTTTCACTTTATCTATATTTAATGCTTCATACATATATTCAAAGATTCGATGTGATGTTTTTGGGAAAAA

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 77.80% 0.10% 0.89% 21.12% NA
All Indica  2759 99.00% 0.00% 0.04% 0.94% NA
All Japonica  1512 39.60% 0.50% 2.58% 57.41% NA
Aus  269 99.30% 0.00% 0.37% 0.37% NA
Indica I  595 99.80% 0.00% 0.00% 0.17% NA
Indica II  465 99.60% 0.00% 0.00% 0.43% NA
Indica III  913 98.90% 0.00% 0.00% 1.10% NA
Indica Intermediate  786 98.20% 0.00% 0.13% 1.65% NA
Temperate Japonica  767 56.80% 0.10% 3.26% 39.77% NA
Tropical Japonica  504 24.40% 0.60% 1.79% 73.21% NA
Japonica Intermediate  241 16.20% 1.20% 2.07% 80.50% NA
VI/Aromatic  96 19.80% 0.00% 1.04% 79.17% NA
Intermediate  90 70.00% 0.00% 0.00% 30.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0221843984 G -> T LOC_Os02g36210.1 intron_variant ; MODIFIER silent_mutation Average:31.536; most accessible tissue: Callus, score: 68.1 N N N N
vg0221843984 G -> DEL N N silent_mutation Average:31.536; most accessible tissue: Callus, score: 68.1 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0221843984 2.06E-06 NA mr1210 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
vg0221843984 1.75E-07 1.75E-07 mr1186_2 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
vg0221843984 5.71E-06 5.71E-06 mr1245_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
vg0221843984 2.97E-07 NA 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
vg0221843984 NA 4.49E-06 mr1329_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
vg0221843984 NA 2.85E-11 mr1379_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
vg0221843984 NA 5.52E-08 mr1554_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
vg0221843984 2.70E-06 2.33E-10 mr1559_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
vg0221843984 NA 1.71E-06 mr1559_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
vg0221843984 4.31E-07 NA mr1585_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
vg0221843984 5.01E-06 NA mr1647_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
vg0221843984 2.17E-07 2.17E-07 mr1647_2 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
vg0221843984 7.40E-06 7.40E-06 mr1655_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
vg0221843984 NA 6.05E-07 mr1691_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
vg0221843984 4.82E-07 2.87E-13 mr1947_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
vg0221843984 NA 1.68E-06 mr1977_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