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Detailed information for vg0809216172:

Variant ID: vg0809216172 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 9216172
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


TGGCATTACCAGACTTTTCTAAAGAATTTGTGGTTGAGACAGATGCTAGTGGTACAGGCATTGGGGCAGTCCTGATGCAAGATGGACACCCACTGGCTTT[C/T]
ATTAGTAAGGCTCTCAGTCCCAGATCTCAAGCTATGTCAACTTATGAAAAGGAATGTATAGCTGTTCTGCTGGCAGTGGATAAATGGAGGCAGTATTTGC

Reverse complement sequence

GCAAATACTGCCTCCATTTATCCACTGCCAGCAGAACAGCTATACATTCCTTTTCATAAGTTGACATAGCTTGAGATCTGGGACTGAGAGCCTTACTAAT[G/A]
AAAGCCAGTGGGTGTCCATCTTGCATCAGGACTGCCCCAATGCCTGTACCACTAGCATCTGTCTCAACCACAAATTCTTTAGAAAAGTCTGGTAATGCCA

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 64.10% 4.10% 1.18% 30.62% NA
All Indica  2759 78.00% 1.40% 1.16% 19.39% NA
All Japonica  1512 45.00% 0.10% 1.32% 53.51% NA
Aus  269 46.10% 53.90% 0.00% 0.00% NA
Indica I  595 80.70% 0.20% 0.50% 18.66% NA
Indica II  465 51.20% 0.60% 1.29% 46.88% NA
Indica III  913 93.00% 0.40% 1.42% 5.15% NA
Indica Intermediate  786 74.40% 4.10% 1.27% 20.23% NA
Temperate Japonica  767 61.10% 0.00% 1.04% 37.81% NA
Tropical Japonica  504 24.40% 0.40% 1.59% 73.61% NA
Japonica Intermediate  241 36.90% 0.00% 1.66% 61.41% NA
VI/Aromatic  96 17.70% 2.10% 3.12% 77.08% NA
Intermediate  90 62.20% 4.40% 1.11% 32.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0809216172 C -> T LOC_Os08g15220.1 synonymous_variant ; p.Phe755Phe; LOW synonymous_codon Average:41.58; most accessible tissue: Minghui63 flag leaf, score: 51.386 N N N N
vg0809216172 C -> DEL LOC_Os08g15220.1 N frameshift_variant Average:41.58; most accessible tissue: Minghui63 flag leaf, score: 51.386 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0809216172 NA 1.12E-15 mr1612 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
vg0809216172 NA 1.16E-07 mr1706 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
vg0809216172 NA 1.67E-07 mr1989 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
vg0809216172 NA 2.05E-08 mr1612_2 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
vg0809216172 4.53E-06 NA mr1746_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