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Detailed information for vg0120215560:

Variant ID: vg0120215560 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 20215560
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGGCGATGCTTGCCTCTGGACGAGCACGGTTACGAATATACTTCTTCGGAATGCCCATGTACCTCTCGAAAGGAAACATGTTGTGTAGGTACACGGGCC[C/T]
GAGAATACCGATCTCTTTGACAAGGTGACAAAGCAGATGCGTCATTATATTGAAAAATGAAGGTGAAAATATCAACTCAAAGCTGACAAGACATTGCAGT

Reverse complement sequence

ACTGCAATGTCTTGTCAGCTTTGAGTTGATATTTTCACCTTCATTTTTCAATATAATGACGCATCTGCTTTGTCACCTTGTCAAAGAGATCGGTATTCTC[G/A]
GGCCCGTGTACCTACACAACATGTTTCCTTTCGAGAGGTACATGGGCATTCCGAAGAAGTATATTCGTAACCGTGCTCGTCCAGAGGCAAGCATCGCCAA

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 98.70% 0.20% 0.61% 0.51% NA
All Indica  2759 97.70% 0.40% 1.05% 0.87% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.30% 0.30% 2.18% 1.18% NA
Indica II  465 98.30% 0.00% 0.43% 1.29% NA
Indica III  913 99.20% 0.10% 0.11% 0.55% NA
Indica Intermediate  786 96.70% 0.90% 1.65% 0.76% 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
vg0120215560 C -> T LOC_Os01g36420.1 missense_variant ; p.Gly655Arg; MODERATE N Average:37.244; most accessible tissue: Minghui63 flag leaf, score: 73.752 N N N N
vg0120215560 C -> T LOC_Os01g36430.1 upstream_gene_variant ; 4907.0bp to feature; MODIFIER N Average:37.244; most accessible tissue: Minghui63 flag leaf, score: 73.752 N N N N
vg0120215560 C -> T LOC_Os01g36410.1 downstream_gene_variant ; 1487.0bp to feature; MODIFIER N Average:37.244; most accessible tissue: Minghui63 flag leaf, score: 73.752 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0120215560 5.84E-06 NA mr1050_2 Ind_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