Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg1003719342:

Variant ID: vg1003719342 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3719342
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: 254. )

Flanking Sequence (100 bp) in Reference Genome:


CTATACTCCCTGCAAAAAAAAAACTGCGAGCCCTCGCCTCGCAGTCGCAGGCAAAAGCGAGAAAGTTGGCAACCTGCCACTGTCAGCAGCAACAAGGACG[G/A]
AGGAGAGGAGGGAAGGAGCAGAGCTATTATCGCTACGTCCACCAAACGACAAGCAACAAAGCAGCAAGTGCATGACATTTGTGGTTCTGTACGCCTAGAA

Reverse complement sequence

TTCTAGGCGTACAGAACCACAAATGTCATGCACTTGCTGCTTTGTTGCTTGTCGTTTGGTGGACGTAGCGATAATAGCTCTGCTCCTTCCCTCCTCTCCT[C/T]
CGTCCTTGTTGCTGCTGACAGTGGCAGGTTGCCAACTTTCTCGCTTTTGCCTGCGACTGCGAGGCGAGGGCTCGCAGTTTTTTTTTTGCAGGGAGTATAG

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 76.50% 1.10% 0.44% 21.98% NA
All Indica  2759 61.90% 0.00% 0.76% 37.33% NA
All Japonica  1512 96.50% 3.40% 0.00% 0.13% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 67.60% 0.00% 1.18% 31.26% NA
Indica II  465 66.20% 0.00% 0.86% 32.90% NA
Indica III  913 50.70% 0.00% 0.44% 48.85% NA
Indica Intermediate  786 67.90% 0.10% 0.76% 31.17% NA
Temperate Japonica  767 95.70% 4.20% 0.00% 0.13% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 93.40% 6.20% 0.00% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 0.00% 0.00% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1003719342 G -> A LOC_Os10g07060.1 downstream_gene_variant ; 2093.0bp to feature; MODIFIER silent_mutation Average:17.889; most accessible tissue: Callus, score: 93.848 N N N N
vg1003719342 G -> A LOC_Os10g07060-LOC_Os10g07080 intergenic_region ; MODIFIER silent_mutation Average:17.889; most accessible tissue: Callus, score: 93.848 N N N N
vg1003719342 G -> DEL N N silent_mutation Average:17.889; most accessible tissue: Callus, score: 93.848 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003719342 NA 8.31E-07 mr1210 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
vg1003719342 5.52E-07 3.97E-06 mr1280 Jap_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
vg1003719342 6.44E-06 6.44E-06 mr1284 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
vg1003719342 9.08E-06 9.08E-06 mr1288 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
vg1003719342 NA 3.10E-06 mr1305 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
vg1003719342 5.52E-06 5.52E-06 mr1307 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
vg1003719342 8.48E-06 8.48E-06 mr1357 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
vg1003719342 NA 2.48E-06 mr1358 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
vg1003719342 NA 6.26E-06 mr1380 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
vg1003719342 3.26E-06 3.26E-06 mr1393 Jap_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
vg1003719342 1.82E-07 1.82E-07 mr1407 Jap_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
vg1003719342 3.21E-09 3.21E-09 mr1505 Jap_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
vg1003719342 NA 5.22E-08 mr1585 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
vg1003719342 7.51E-06 NA mr1611 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
vg1003719342 6.52E-06 6.52E-06 mr1710 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
vg1003719342 1.26E-06 1.71E-07 mr1736 Jap_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
vg1003719342 2.74E-06 NA mr1788 Jap_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
vg1003719342 6.89E-06 6.89E-06 mr1849 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
vg1003719342 3.57E-06 3.57E-06 mr1955 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
vg1003719342 7.63E-06 7.63E-06 mr1967 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
vg1003719342 3.90E-07 3.90E-07 mr1978 Jap_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
vg1003719342 NA 1.44E-06 mr1098_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
vg1003719342 NA 3.57E-06 mr1305_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
vg1003719342 NA 1.05E-07 mr1585_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
vg1003719342 5.48E-06 5.48E-06 mr1647_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