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Detailed information for vg1019348557:

Variant ID: vg1019348557 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 19348557
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCTTCTCTTCCGAGCGATTCAGACCGGTCATCTCCATGCATTGTGTGTGAAAGAAACTGTGAACAGCTAATCAAAATCAAGGTGCACGCCGAAATTGCCA[A/G]
ATGTAACAGATGACTACTTACTCCCTCCGTTTCATGAGATAAATCATTCTAGCACTTTCCACATTCATCAAGTTATTATAGCCCTTCTTATATTTATCAC

Reverse complement sequence

GTGATAAATATAAGAAGGGCTATAATAACTTGATGAATGTGGAAAGTGCTAGAATGATTTATCTCATGAAACGGAGGGAGTAAGTAGTCATCTGTTACAT[T/C]
TGGCAATTTCGGCGTGCACCTTGATTTTGATTAGCTGTTCACAGTTTCTTTCACACACAATGCATGGAGATGACCGGTCTGAATCGCTCGGAAGAGAAGC

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 97.70% 1.50% 0.76% 0.00% NA
All Indica  2759 99.20% 0.00% 0.80% 0.00% NA
All Japonica  1512 94.50% 4.70% 0.79% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.80% 0.00% 3.19% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.00% 0.38% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 85.30% 12.70% 1.98% 0.00% NA
Japonica Intermediate  241 96.30% 2.90% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 0.00% 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
vg1019348557 A -> G LOC_Os10g36190.1 upstream_gene_variant ; 1604.0bp to feature; MODIFIER silent_mutation Average:70.052; most accessible tissue: Callus, score: 90.244 N N N N
vg1019348557 A -> G LOC_Os10g36180.1 downstream_gene_variant ; 251.0bp to feature; MODIFIER silent_mutation Average:70.052; most accessible tissue: Callus, score: 90.244 N N N N
vg1019348557 A -> G LOC_Os10g36200.1 downstream_gene_variant ; 4421.0bp to feature; MODIFIER silent_mutation Average:70.052; most accessible tissue: Callus, score: 90.244 N N N N
vg1019348557 A -> G LOC_Os10g36200.2 downstream_gene_variant ; 4421.0bp to feature; MODIFIER silent_mutation Average:70.052; most accessible tissue: Callus, score: 90.244 N N N N
vg1019348557 A -> G LOC_Os10g36180-LOC_Os10g36190 intergenic_region ; MODIFIER silent_mutation Average:70.052; most accessible tissue: Callus, score: 90.244 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1019348557 NA 1.80E-06 mr1218 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
vg1019348557 NA 2.37E-07 mr1583 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
vg1019348557 2.18E-06 1.17E-07 mr1794 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
vg1019348557 NA 5.04E-06 mr1850_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