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Detailed information for vg0827595612:

Variant ID: vg0827595612 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 27595612
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGGAAACCGAATCGGCCAGTCGGAATTTTTTCGGAATTTCTCGGAATCGGAATCGAAAACGGAAATATTTTCTCGGAAACGGAATCGAATATGATAATAG[C/T]
AGTTTCCGTCGGAACCCGGAAACGATCGGAAACATTCCAGAAAAATTGTCGGAATTTCCGAAGTTAAAAAGCCCATAGATTCAATAGTCCATAATTCATC

Reverse complement sequence

GATGAATTATGGACTATTGAATCTATGGGCTTTTTAACTTCGGAAATTCCGACAATTTTTCTGGAATGTTTCCGATCGTTTCCGGGTTCCGACGGAAACT[G/A]
CTATTATCATATTCGATTCCGTTTCCGAGAAAATATTTCCGTTTTCGATTCCGATTCCGAGAAATTCCGAAAAAATTCCGACTGGCCGATTCGGTTTCCG

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 96.20% 1.90% 1.88% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 88.50% 5.80% 5.69% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 78.50% 11.20% 10.30% 0.00% NA
Tropical Japonica  504 99.20% 0.00% 0.79% 0.00% NA
Japonica Intermediate  241 97.90% 0.80% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 3.30% 3.33% 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
vg0827595612 C -> T LOC_Os08g43640.1 upstream_gene_variant ; 3546.0bp to feature; MODIFIER silent_mutation Average:22.128; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0827595612 C -> T LOC_Os08g43640.2 upstream_gene_variant ; 3581.0bp to feature; MODIFIER silent_mutation Average:22.128; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0827595612 C -> T LOC_Os08g43654.1 intron_variant ; MODIFIER silent_mutation Average:22.128; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0827595612 4.87E-06 NA mr1926 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