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Detailed information for vg0320639721:

Variant ID: vg0320639721 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 20639721
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCAAAATATGATCTTGCTTTCCTGTTGAATCAATTAACAATGAAAGATATTACACCCAGGAATTTGCTTTGATGAAGTCGGATCCCCCAATCGCTCAACG[T/C]
CGATCTCCCCGCCACCAAACTGGGCAAGGGAGCGGAGGACCAAGAATTCGGTCTGAACCTCAACCAAGTGCTTCTGATCCAGTCGGCCAGTCAGACTCTC

Reverse complement sequence

GAGAGTCTGACTGGCCGACTGGATCAGAAGCACTTGGTTGAGGTTCAGACCGAATTCTTGGTCCTCCGCTCCCTTGCCCAGTTTGGTGGCGGGGAGATCG[A/G]
CGTTGAGCGATTGGGGGATCCGACTTCATCAAAGCAAATTCCTGGGTGTAATATCTTTCATTGTTAATTGATTCAACAGGAAAGCAAGATCATATTTTGA

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 67.50% 32.40% 0.11% 0.00% NA
All Indica  2759 97.40% 2.50% 0.07% 0.00% NA
All Japonica  1512 12.70% 87.20% 0.07% 0.00% NA
Aus  269 88.80% 11.20% 0.00% 0.00% NA
Indica I  595 98.70% 1.30% 0.00% 0.00% NA
Indica II  465 97.00% 3.00% 0.00% 0.00% NA
Indica III  913 98.60% 1.40% 0.00% 0.00% NA
Indica Intermediate  786 95.40% 4.30% 0.25% 0.00% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 33.90% 65.90% 0.20% 0.00% NA
Japonica Intermediate  241 7.90% 92.10% 0.00% 0.00% NA
VI/Aromatic  96 27.10% 72.90% 0.00% 0.00% NA
Intermediate  90 47.80% 50.00% 2.22% 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
vg0320639721 T -> C LOC_Os03g37240.1 synonymous_variant ; p.Arg299Arg; LOW synonymous_codon Average:43.148; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0320639721 NA 6.14E-08 mr1217 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
vg0320639721 1.12E-06 2.18E-09 mr1718 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
vg0320639721 NA 1.21E-07 mr1750 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
vg0320639721 NA 5.84E-06 mr1830 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
vg0320639721 NA 2.45E-07 mr1845 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