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Detailed information for vg1004077040:

Variant ID: vg1004077040 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4077040
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTTCACTATCTCTATTCGTCCACCAATATAAGGGATTCTAGAGTACTACTTATCCCATCAATCACATTGATTTCATTAAAAAAATTCGTATTATCCCC[G/A]
ACTACACTCACACATTCAGCATCTCATTTAACCAAGGGCATCATTGTTTTTCTCTGCATACCCAAAGTCTGTAGTATTTGTTGATGGAGGGAATACACAA

Reverse complement sequence

TTGTGTATTCCCTCCATCAACAAATACTACAGACTTTGGGTATGCAGAGAAAAACAATGATGCCCTTGGTTAAATGAGATGCTGAATGTGTGAGTGTAGT[C/T]
GGGGATAATACGAATTTTTTTAATGAAATCAATGTGATTGATGGGATAAGTAGTACTCTAGAATCCCTTATATTGGTGGACGAATAGAGATAGTGAAAAT

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 68.00% 32.00% 0.00% 0.00% NA
All Indica  2759 83.60% 16.40% 0.00% 0.00% NA
All Japonica  1512 39.40% 60.60% 0.00% 0.00% NA
Aus  269 96.30% 3.70% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 85.60% 14.40% 0.00% 0.00% NA
Indica III  913 68.50% 31.50% 0.00% 0.00% NA
Indica Intermediate  786 88.30% 11.70% 0.00% 0.00% NA
Temperate Japonica  767 22.00% 78.00% 0.00% 0.00% NA
Tropical Japonica  504 74.40% 25.60% 0.00% 0.00% NA
Japonica Intermediate  241 21.20% 78.80% 0.00% 0.00% NA
VI/Aromatic  96 3.10% 96.90% 0.00% 0.00% NA
Intermediate  90 57.80% 42.20% 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
vg1004077040 G -> A LOC_Os10g07554.1 downstream_gene_variant ; 3098.0bp to feature; MODIFIER silent_mutation Average:39.674; most accessible tissue: Callus, score: 70.731 N N N N
vg1004077040 G -> A LOC_Os10g07556.1 intron_variant ; MODIFIER silent_mutation Average:39.674; most accessible tissue: Callus, score: 70.731 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004077040 NA 6.22E-09 mr1023 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
vg1004077040 NA 7.78E-08 mr1489 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
vg1004077040 NA 1.55E-10 mr1491 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
vg1004077040 NA 2.57E-08 mr1379_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
vg1004077040 NA 1.87E-07 mr1401_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
vg1004077040 NA 1.96E-09 mr1559_2 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
vg1004077040 NA 1.31E-06 mr1606_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
vg1004077040 NA 3.34E-10 mr1942_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