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Detailed information for vg0221815577:

Variant ID: vg0221815577 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 21815577
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATATTCAAATAAGTATAGACATTTCACCCATAGTAAACCATAGGCAATTTGTTAGTAGTTCAAAAGATATATTCTGAAACCGTTAAAAAAATATCACTA[C/T]
TAGAGAAACTCTCATCTCTCCCGGTTTGCAATCCCCTGTAGTCCCGGGTTACAAACAAAGAGAGAGAATCCAGGACTAAAAATGGCGATCTTTAGTCCGG

Reverse complement sequence

CCGGACTAAAGATCGCCATTTTTAGTCCTGGATTCTCTCTCTTTGTTTGTAACCCGGGACTACAGGGGATTGCAAACCGGGAGAGATGAGAGTTTCTCTA[G/A]
TAGTGATATTTTTTTAACGGTTTCAGAATATATCTTTTGAACTACTAACAAATTGCCTATGGTTTACTATGGGTGAAATGTCTATACTTATTTGAATATA

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 93.20% 5.70% 1.10% 0.00% NA
All Indica  2759 99.30% 0.70% 0.04% 0.00% NA
All Japonica  1512 86.80% 10.00% 3.17% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 98.80% 1.20% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.80% 0.13% 0.00% NA
Temperate Japonica  767 97.90% 0.30% 1.83% 0.00% NA
Tropical Japonica  504 73.80% 23.00% 3.17% 0.00% NA
Japonica Intermediate  241 78.80% 13.70% 7.47% 0.00% NA
VI/Aromatic  96 12.50% 84.40% 3.12% 0.00% NA
Intermediate  90 78.90% 21.10% 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
vg0221815577 C -> T LOC_Os02g36190.1 upstream_gene_variant ; 2117.0bp to feature; MODIFIER silent_mutation Average:38.054; most accessible tissue: Callus, score: 58.262 N N N N
vg0221815577 C -> T LOC_Os02g36190-LOC_Os02g36200 intergenic_region ; MODIFIER silent_mutation Average:38.054; most accessible tissue: Callus, score: 58.262 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0221815577 1.99E-08 NA mr1042_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
vg0221815577 8.04E-08 NA mr1042_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
vg0221815577 NA 9.53E-06 mr1150_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
vg0221815577 1.15E-06 NA mr1742_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
vg0221815577 1.19E-10 NA mr1871_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
vg0221815577 4.00E-08 NA mr1871_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