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Detailed information for vg0617709303:

Variant ID: vg0617709303 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 17709303
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCACCGCTTCAATTTCACCCGCCGCTAGCTTTGTAGGCTCTGCTTGTACAGGCTCTGATGGTTCTTCTGCATCCTTTAATGTCTGAGGTGATGCAACGGG[A/T]
GGCTCCGGTACTGGAGGTGATGTAACTGGTGGCTCTGGTACTGGAGGTGATGCAACTGGTGGCTCTGGTCCTCGAGGTGATGCAACTGGTGGCTCTGGTC

Reverse complement sequence

GACCAGAGCCACCAGTTGCATCACCTCGAGGACCAGAGCCACCAGTTGCATCACCTCCAGTACCAGAGCCACCAGTTACATCACCTCCAGTACCGGAGCC[T/A]
CCCGTTGCATCACCTCAGACATTAAAGGATGCAGAAGAACCATCAGAGCCTGTACAAGCAGAGCCTACAAAGCTAGCGGCGGGTGAAATTGAAGCGGTGC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.10% 0.50% 0.95% 46.53% NA
All Indica  2759 24.90% 0.00% 1.09% 74.01% NA
All Japonica  1512 96.20% 1.30% 0.60% 1.92% NA
Aus  269 62.50% 0.00% 1.12% 36.43% NA
Indica I  595 23.40% 0.00% 0.50% 76.13% NA
Indica II  465 10.10% 0.00% 1.94% 87.96% NA
Indica III  913 26.00% 0.10% 1.64% 72.29% NA
Indica Intermediate  786 33.50% 0.00% 0.38% 66.16% NA
Temperate Japonica  767 96.70% 0.00% 0.39% 2.87% NA
Tropical Japonica  504 95.80% 3.00% 0.40% 0.79% NA
Japonica Intermediate  241 95.40% 1.70% 1.66% 1.24% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 61.10% 2.20% 3.33% 33.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0617709303 A -> T LOC_Os06g30610.1 synonymous_variant ; p.Pro650Pro; LOW synonymous_codon Average:8.886; most accessible tissue: Callus, score: 16.543 N N N N
vg0617709303 A -> DEL LOC_Os06g30610.1 N frameshift_variant Average:8.886; most accessible tissue: Callus, score: 16.543 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0617709303 NA 3.32E-21 mr1301 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
vg0617709303 NA 4.23E-06 mr1408 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
vg0617709303 3.77E-07 5.21E-21 mr1518 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
vg0617709303 NA 5.33E-08 mr1518 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
vg0617709303 5.71E-06 3.04E-21 mr1676 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
vg0617709303 NA 9.78E-07 mr1676 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
vg0617709303 NA 1.45E-06 mr1993 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
vg0617709303 NA 8.41E-21 mr1301_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
vg0617709303 1.05E-06 NA mr1676_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
vg0617709303 NA 2.41E-14 mr1769_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
vg0617709303 NA 2.83E-10 mr1993_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