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Detailed information for vg0817027394:

Variant ID: vg0817027394 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 17027394
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


TGATCTCGGCCGGCCAACACACTCTCCAGGTCTGCTCAACACAGAAATGACTAAGTCAAGTCATTCTCCTCTTTCGAGAACACGACAAATTAATTCGATC[C/T]
GAACAAAAGAGCCAAGGAGATGAAGACTAAAAGTACCAACCTAAGAAAGTCATCGCCATGTCCGCCTCCCCGGACAGGCTTTGATCGATATCGTCCCGCT

Reverse complement sequence

AGCGGGACGATATCGATCAAAGCCTGTCCGGGGAGGCGGACATGGCGATGACTTTCTTAGGTTGGTACTTTTAGTCTTCATCTCCTTGGCTCTTTTGTTC[G/A]
GATCGAATTAATTTGTCGTGTTCTCGAAAGAGGAGAATGACTTGACTTAGTCATTTCTGTGTTGAGCAGACCTGGAGAGTGTGTTGGCCGGCCGAGATCA

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 95.50% 2.60% 1.82% 0.00% NA
All Indica  2759 93.90% 3.30% 2.83% 0.00% NA
All Japonica  1512 97.20% 2.20% 0.53% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 84.40% 7.10% 8.57% 0.00% NA
Indica II  465 96.60% 3.00% 0.43% 0.00% NA
Indica III  913 99.80% 0.00% 0.22% 0.00% NA
Indica Intermediate  786 92.60% 4.50% 2.93% 0.00% NA
Temperate Japonica  767 99.70% 0.00% 0.26% 0.00% NA
Tropical Japonica  504 92.90% 6.30% 0.79% 0.00% NA
Japonica Intermediate  241 98.30% 0.80% 0.83% 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
vg0817027394 C -> T LOC_Os08g27920.1 downstream_gene_variant ; 4750.0bp to feature; MODIFIER silent_mutation Average:53.538; most accessible tissue: Minghui63 flag leaf, score: 69.681 N N N N
vg0817027394 C -> T LOC_Os08g27930.1 downstream_gene_variant ; 777.0bp to feature; MODIFIER silent_mutation Average:53.538; most accessible tissue: Minghui63 flag leaf, score: 69.681 N N N N
vg0817027394 C -> T LOC_Os08g27940.1 intron_variant ; MODIFIER silent_mutation Average:53.538; most accessible tissue: Minghui63 flag leaf, score: 69.681 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0817027394 NA 2.57E-07 mr1038 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
vg0817027394 NA 3.07E-07 mr1038 Ind_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
vg0817027394 NA 5.52E-06 mr1376 Ind_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
vg0817027394 NA 1.97E-07 mr1389 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
vg0817027394 NA 2.01E-07 mr1389 Ind_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
vg0817027394 NA 5.52E-06 mr1431 Ind_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
vg0817027394 1.92E-06 6.39E-06 mr1528 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
vg0817027394 NA 5.74E-06 mr1627 Ind_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
vg0817027394 NA 2.57E-08 mr1038_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
vg0817027394 NA 2.61E-08 mr1038_2 Ind_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
vg0817027394 NA 3.28E-06 mr1389_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
vg0817027394 NA 1.87E-06 mr1389_2 Ind_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