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Detailed information for vg1122364508:

Variant ID: vg1122364508 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 22364508
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTAAGTGTCTTTTAAATGCTGTTTACTGCAAAACCTAACCCCTATACTATAACACCATTGTACTCCTTTGCATTTATGTTGCACTTGTGGGTGTGTCTTG[T/G]
TTAGTACGGTGGTTGTACTCAGTCTTGCTCAATTTTTCCCAAACCCAGAAGAGGAGCTCCTGGATGATGAAGGCTTTGGTGTTTAGCTCATGCCTGCCGT

Reverse complement sequence

ACGGCAGGCATGAGCTAAACACCAAAGCCTTCATCATCCAGGAGCTCCTCTTCTGGGTTTGGGAAAAATTGAGCAAGACTGAGTACAACCACCGTACTAA[A/C]
CAAGACACACCCACAAGTGCAACATAAATGCAAAGGAGTACAATGGTGTTATAGTATAGGGGTTAGGTTTTGCAGTAAACAGCATTTAAAAGACACTTAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 43.50% 9.40% 1.44% 45.60% NA
All Indica  2759 39.10% 0.40% 2.21% 58.21% NA
All Japonica  1512 51.30% 26.70% 0.20% 21.89% NA
Aus  269 28.30% 7.80% 1.49% 62.45% NA
Indica I  595 46.90% 0.00% 1.01% 52.10% NA
Indica II  465 24.70% 0.20% 4.30% 70.75% NA
Indica III  913 46.30% 0.20% 1.20% 52.25% NA
Indica Intermediate  786 33.50% 1.10% 3.05% 62.34% NA
Temperate Japonica  767 75.20% 13.80% 0.26% 10.69% NA
Tropical Japonica  504 21.20% 42.90% 0.00% 35.91% NA
Japonica Intermediate  241 37.80% 33.60% 0.41% 28.22% NA
VI/Aromatic  96 84.40% 2.10% 0.00% 13.54% NA
Intermediate  90 51.10% 7.80% 0.00% 41.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1122364508 T -> DEL N N silent_mutation Average:9.695; most accessible tissue: Callus, score: 31.452 N N N N
vg1122364508 T -> G LOC_Os11g37780.1 upstream_gene_variant ; 2470.0bp to feature; MODIFIER silent_mutation Average:9.695; most accessible tissue: Callus, score: 31.452 N N N N
vg1122364508 T -> G LOC_Os11g37774-LOC_Os11g37780 intergenic_region ; MODIFIER silent_mutation Average:9.695; most accessible tissue: Callus, score: 31.452 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1122364508 NA 8.34E-06 mr1148 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
vg1122364508 NA 1.29E-07 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
vg1122364508 NA 1.15E-06 mr1338 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
vg1122364508 NA 9.60E-07 mr1418 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
vg1122364508 5.02E-06 NA mr1617 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
vg1122364508 NA 6.77E-07 mr1627 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
vg1122364508 NA 8.86E-08 mr1797 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
vg1122364508 NA 8.86E-08 mr1801 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
vg1122364508 2.18E-06 NA mr1917 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
vg1122364508 NA 1.69E-06 mr1991 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
vg1122364508 NA 1.93E-06 mr1992 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