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Detailed information for vg1000967617:

Variant ID: vg1000967617 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 967617
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:


AAGCTGGTTGATGGAAGATATGTTGTTTCCATTCACCCCACCATCTGTCAAAGTTCCAGCTCCTGAGCCTTGCCAGCTCTATGTTCTCAATACTGCCCAA[G/A]
GGGGGTCCTGGGATGTTGAGTAGCCGATCCATCATCAGAGTTGATGAAATTTCTCCTCGGCACTGGATTTTGTCAGCAAAGAATAAGCCGATTGGGAGTT

Reverse complement sequence

AACTCCCAATCGGCTTATTCTTTGCTGACAAAATCCAGTGCCGAGGAGAAATTTCATCAACTCTGATGATGGATCGGCTACTCAACATCCCAGGACCCCC[C/T]
TTGGGCAGTATTGAGAACATAGAGCTGGCAAGGCTCAGGAGCTGGAACTTTGACAGATGGTGGGGTGAATGGAAACAACATATCTTCCATCAACCAGCTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 39.00% 33.10% 2.52% 25.35% NA
All Indica  2759 63.10% 2.20% 3.26% 31.50% NA
All Japonica  1512 4.10% 90.00% 0.66% 5.22% NA
Aus  269 8.90% 3.30% 4.46% 83.27% NA
Indica I  595 22.20% 2.90% 4.03% 70.92% NA
Indica II  465 88.40% 1.50% 0.86% 9.25% NA
Indica III  913 77.80% 0.80% 2.96% 18.51% NA
Indica Intermediate  786 62.00% 3.70% 4.45% 29.90% NA
Temperate Japonica  767 0.70% 97.80% 0.39% 1.17% NA
Tropical Japonica  504 9.70% 82.30% 1.19% 6.75% NA
Japonica Intermediate  241 3.30% 81.30% 0.41% 14.94% NA
VI/Aromatic  96 6.20% 88.50% 1.04% 4.17% NA
Intermediate  90 12.20% 56.70% 6.67% 24.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1000967617 G -> A LOC_Os10g02560.1 synonymous_variant ; p.Pro312Pro; LOW synonymous_codon Average:10.111; most accessible tissue: Callus, score: 30.081 N N N N
vg1000967617 G -> A LOC_Os10g02560.1 synonymous_variant ; p.Pro312Pro; LOW nonsynonymous_codon ; P312S Average:10.111; most accessible tissue: Callus, score: 30.081 benign 0.852 DELETERIOUS 0.05
vg1000967617 G -> DEL LOC_Os10g02560.1 N frameshift_variant Average:10.111; most accessible tissue: Callus, score: 30.081 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1000967617 NA 2.88E-07 mr1527 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
vg1000967617 NA 4.43E-11 mr1623 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
vg1000967617 NA 1.75E-11 mr1322_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
vg1000967617 NA 6.23E-17 mr1324_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
vg1000967617 NA 4.29E-13 mr1325_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
vg1000967617 NA 1.32E-16 mr1326_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
vg1000967617 NA 1.14E-14 mr1333_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
vg1000967617 NA 2.18E-19 mr1336_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
vg1000967617 NA 1.34E-08 mr1449_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
vg1000967617 NA 2.16E-08 mr1527_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
vg1000967617 NA 5.91E-08 mr1623_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
vg1000967617 NA 2.44E-08 mr1690_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
vg1000967617 NA 1.03E-16 mr1744_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