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Detailed information for vg0102760349:

Variant ID: vg0102760349 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 2760349
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


TTTGGAAAGAATGCAACGGCCGGGTTTTCAATCAGCAACAAAGGACCTGGGTGGACATCGTGAAGGGAATGGCGGCAGAGACGGCACTCTGGCGCCAAGC[G/A]
AATTCAGCCATCCCTGCTCTGATCCTCAGAAGGGACTTCGGTAGCCAAAACAGACCGTGAGAGATAAACCTTTGATTTTGTACTTTGAGTCCTGTTTCAG

Reverse complement sequence

CTGAAACAGGACTCAAAGTACAAAATCAAAGGTTTATCTCTCACGGTCTGTTTTGGCTACCGAAGTCCCTTCTGAGGATCAGAGCAGGGATGGCTGAATT[C/T]
GCTTGGCGCCAGAGTGCCGTCTCTGCCGCCATTCCCTTCACGATGTCCACCCAGGTCCTTTGTTGCTGATTGAAAACCCGGCCGTTGCATTCTTTCCAAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.40% 5.10% 1.42% 0.00% NA
All Indica  2759 99.30% 0.50% 0.18% 0.00% NA
All Japonica  1512 81.40% 14.60% 3.97% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.00% 0.50% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.60% 1.10% 0.25% 0.00% NA
Temperate Japonica  767 96.50% 1.40% 2.09% 0.00% NA
Tropical Japonica  504 53.00% 40.10% 6.94% 0.00% NA
Japonica Intermediate  241 92.90% 3.30% 3.73% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 8.90% 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
vg0102760349 G -> A LOC_Os01g05780.1 synonymous_variant ; p.Ala99Ala; LOW synonymous_codon Average:51.713; most accessible tissue: Minghui63 root, score: 65.279 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0102760349 NA 1.13E-06 mr1248 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
vg0102760349 1.91E-06 1.36E-29 mr1699 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
vg0102760349 NA 8.84E-12 mr1769 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
vg0102760349 NA 2.32E-13 mr1769 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
vg0102760349 NA 2.54E-12 mr1769_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
vg0102760349 NA 1.94E-09 mr1916_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