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Detailed information for vg0817970097:

Variant ID: vg0817970097 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 17970097
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTCGCGTTTATCCTAATACATCTTTTTGTATGTTGCAGAAAAGACGTTGTCGTCATCGTCTCTCAAGCCAGAGTGGTAGCTAGCCCTCGAAGGAATTCA[C/T]
GCAGGCAAGTGATGTAAATATATGATTGTTAGATTTTTAATGCAATTAAGACTATTAGATTTAATATACGACACTTAGACTTAGCATTATAATTAGAGTT

Reverse complement sequence

AACTCTAATTATAATGCTAAGTCTAAGTGTCGTATATTAAATCTAATAGTCTTAATTGCATTAAAAATCTAACAATCATATATTTACATCACTTGCCTGC[G/A]
TGAATTCCTTCGAGGGCTAGCTACCACTCTGGCTTGAGAGACGATGACGACAACGTCTTTTCTGCAACATACAAAAAGATGTATTAGGATAAACGCGAAG

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 92.60% 0.80% 0.49% 6.14% NA
All Indica  2759 88.30% 0.70% 0.83% 10.22% NA
All Japonica  1512 99.70% 0.00% 0.00% 0.33% NA
Aus  269 92.60% 7.40% 0.00% 0.00% NA
Indica I  595 91.80% 2.50% 0.67% 5.04% NA
Indica II  465 98.50% 0.00% 0.00% 1.51% NA
Indica III  913 84.60% 0.00% 1.64% 13.80% NA
Indica Intermediate  786 84.00% 0.40% 0.51% 15.14% NA
Temperate Japonica  767 99.70% 0.00% 0.00% 0.26% NA
Tropical Japonica  504 99.40% 0.00% 0.00% 0.60% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 0.00% 0.00% 2.08% NA
Intermediate  90 98.90% 0.00% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0817970097 C -> T LOC_Os08g29290.1 intron_variant ; MODIFIER silent_mutation Average:21.419; most accessible tissue: Zhenshan97 flag leaf, score: 31.305 N N N N
vg0817970097 C -> DEL N N silent_mutation Average:21.419; most accessible tissue: Zhenshan97 flag leaf, score: 31.305 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0817970097 2.12E-08 2.12E-08 mr1240 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