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Detailed information for vg0316036597:

Variant ID: vg0316036597 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16036597
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:


CACAGACAACACACATTAACAATAGCATGTACACAACCCATTGCCGCAGGACTTCTCTACTTCCAAATTTTTCTTCATCTCTGTATGTTCTCTCTTAGAG[C/T]
AAGGCTAGTGTTAACAGTGAAATTTGGTAAGCCCGGAGTAGTCATCAGCTTAGAATCAGCATCGGCTTCGAAGTCCTGAGATTAGCCGATGAGAGCTGTC

Reverse complement sequence

GACAGCTCTCATCGGCTAATCTCAGGACTTCGAAGCCGATGCTGATTCTAAGCTGATGACTACTCCGGGCTTACCAAATTTCACTGTTAACACTAGCCTT[G/A]
CTCTAAGAGAGAACATACAGAGATGAAGAAAAATTTGGAAGTAGAGAAGTCCTGCGGCAATGGGTTGTGTACATGCTATTGTTAATGTGTGTTGTCTGTG

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 97.20% 2.10% 0.66% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 91.50% 6.40% 2.05% 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 96.00% 2.00% 2.09% 0.00% NA
Tropical Japonica  504 96.20% 3.60% 0.20% 0.00% NA
Japonica Intermediate  241 67.60% 26.60% 5.81% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0316036597 C -> T LOC_Os03g27920.1 upstream_gene_variant ; 2129.0bp to feature; MODIFIER silent_mutation Average:50.584; most accessible tissue: Zhenshan97 young leaf, score: 63.096 N N N N
vg0316036597 C -> T LOC_Os03g27930.1 upstream_gene_variant ; 2396.0bp to feature; MODIFIER silent_mutation Average:50.584; most accessible tissue: Zhenshan97 young leaf, score: 63.096 N N N N
vg0316036597 C -> T LOC_Os03g27910.1 downstream_gene_variant ; 4450.0bp to feature; MODIFIER silent_mutation Average:50.584; most accessible tissue: Zhenshan97 young leaf, score: 63.096 N N N N
vg0316036597 C -> T LOC_Os03g27920-LOC_Os03g27930 intergenic_region ; MODIFIER silent_mutation Average:50.584; most accessible tissue: Zhenshan97 young leaf, score: 63.096 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316036597 7.71E-06 NA mr1023_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
vg0316036597 9.92E-06 9.92E-06 mr1065_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
vg0316036597 1.61E-06 NA mr1079_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