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Detailed information for vg0213593475:

Variant ID: vg0213593475 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 13593475
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAGACCAACAAGCAGAGCAACGTTCCCGGTGAGACTTCAGCTAGTAGGAACTAAAGGGACAAGTCAGTCAGGTTTGAATGATGGAAGCAACAATAGTTC[C/T]
AGTCAAGACCTCTACTTTTCAGGTCTAAAAGGCAGTTCTAATCAGCAGCAGTCTACAATGGTTTGATTTTGTAGTACTTCTCATTGTACATATATGTTTA

Reverse complement sequence

TAAACATATATGTACAATGAGAAGTACTACAAAATCAAACCATTGTAGACTGCTGCTGATTAGAACTGCCTTTTAGACCTGAAAAGTAGAGGTCTTGACT[G/A]
GAACTATTGTTGCTTCCATCATTCAAACCTGACTGACTTGTCCCTTTAGTTCCTACTAGCTGAAGTCTCACCGGGAACGTTGCTCTGCTTGTTGGTCTTC

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 99.80% 0.10% 0.13% 0.00% NA
All Indica  2759 99.80% 0.10% 0.07% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 97.80% 0.70% 1.49% 0.00% NA
Indica I  595 99.70% 0.20% 0.17% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0213593475 C -> T LOC_Os02g22800.1 upstream_gene_variant ; 4620.0bp to feature; MODIFIER N Average:30.178; most accessible tissue: Minghui63 root, score: 47.894 N N N N
vg0213593475 C -> T LOC_Os02g22810.1 downstream_gene_variant ; 321.0bp to feature; MODIFIER N Average:30.178; most accessible tissue: Minghui63 root, score: 47.894 N N N N
vg0213593475 C -> T LOC_Os02g22810-LOC_Os02g22820 intergenic_region ; MODIFIER N Average:30.178; most accessible tissue: Minghui63 root, score: 47.894 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0213593475 NA 6.43E-06 mr1036 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
vg0213593475 6.23E-06 1.52E-07 mr1207 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
vg0213593475 6.60E-06 6.59E-06 mr1306 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
vg0213593475 NA 9.53E-06 mr1617 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
vg0213593475 6.95E-06 2.05E-08 mr1659 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
vg0213593475 NA 2.40E-08 mr1806 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