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Detailed information for vg1016324780:

Variant ID: vg1016324780 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 16324780
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: 295. )

Flanking Sequence (100 bp) in Reference Genome:


AGACGGGTACATAGGAGAGAGGGCCGCTGTTGTAGTTGCTCATCATAGTCGTCTGCCCACCACCATCGAGGCCAGATCTAGCCACCCTCAAGCTCATGTT[G/A]
GCCTTATCTGGTAGCCCTCAAGCTCATGGTGGTTAGATCTTGCCATCCTCAAGCTCATGGCGGACGACTGGCCCATGGAAAAGTTGAAGCTGGCTGACCA

Reverse complement sequence

TGGTCAGCCAGCTTCAACTTTTCCATGGGCCAGTCGTCCGCCATGAGCTTGAGGATGGCAAGATCTAACCACCATGAGCTTGAGGGCTACCAGATAAGGC[C/T]
AACATGAGCTTGAGGGTGGCTAGATCTGGCCTCGATGGTGGTGGGCAGACGACTATGATGAGCAACTACAACAGCGGCCCTCTCTCCTATGTACCCGTCT

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 93.30% 6.60% 0.11% 0.00% NA
All Indica  2759 89.00% 10.80% 0.18% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 87.60% 12.10% 0.34% 0.00% NA
Indica II  465 93.10% 6.70% 0.22% 0.00% NA
Indica III  913 88.90% 11.10% 0.00% 0.00% NA
Indica Intermediate  786 87.80% 12.00% 0.25% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg1016324780 G -> A LOC_Os10g31170.1 intron_variant ; MODIFIER silent_mutation Average:61.818; most accessible tissue: Zhenshan97 panicle, score: 75.67 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1016324780 NA 1.82E-08 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
vg1016324780 NA 5.77E-08 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
vg1016324780 3.86E-06 3.85E-06 mr1288 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
vg1016324780 NA 7.15E-09 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
vg1016324780 NA 2.45E-08 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
vg1016324780 NA 3.64E-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
vg1016324780 NA 2.00E-07 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
vg1016324780 NA 5.25E-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
vg1016324780 NA 2.34E-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