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Detailed information for vg1019669777:

Variant ID: vg1019669777 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 19669777
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTTAGTCCCAGATTGTGCGTCCCAGTTGCTGAACTGGACTAAAAACAGTTGCGAACCGGGACTAGCTTTGTTTCTATCGGTTTTACTAGTTTTCATTAA[G/A]
TCAGTGAGGAGCGGTTCCAACTCCATCCATGCCCACCACGAACCTCTCCGGTGAGAAATTTTCCGGCTCTACAATTTTCGGTTCTGTTTTCGGGGAAAAT

Reverse complement sequence

ATTTTCCCCGAAAACAGAACCGAAAATTGTAGAGCCGGAAAATTTCTCACCGGAGAGGTTCGTGGTGGGCATGGATGGAGTTGGAACCGCTCCTCACTGA[C/T]
TTAATGAAAACTAGTAAAACCGATAGAAACAAAGCTAGTCCCGGTTCGCAACTGTTTTTAGTCCAGTTCAGCAACTGGGACGCACAATCTGGGACTAAAG

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 86.30% 12.80% 0.95% 0.00% NA
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 59.00% 38.00% 2.98% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.30% 1.70% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 28.80% 67.10% 4.04% 0.00% NA
Tropical Japonica  504 96.80% 2.40% 0.79% 0.00% NA
Japonica Intermediate  241 75.90% 19.90% 4.15% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg1019669777 G -> A LOC_Os10g36729.1 upstream_gene_variant ; 860.0bp to feature; MODIFIER silent_mutation Average:45.619; most accessible tissue: Zhenshan97 young leaf, score: 66.83 N N N N
vg1019669777 G -> A LOC_Os10g36740.1 upstream_gene_variant ; 1738.0bp to feature; MODIFIER silent_mutation Average:45.619; most accessible tissue: Zhenshan97 young leaf, score: 66.83 N N N N
vg1019669777 G -> A LOC_Os10g36729-LOC_Os10g36740 intergenic_region ; MODIFIER silent_mutation Average:45.619; most accessible tissue: Zhenshan97 young leaf, score: 66.83 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1019669777 3.63E-07 NA mr1208 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
vg1019669777 NA 9.45E-07 mr1401 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
vg1019669777 NA 1.93E-07 mr1606 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
vg1019669777 NA 7.57E-06 mr1606 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
vg1019669777 NA 4.56E-08 mr1446_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
vg1019669777 NA 7.33E-06 mr1446_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
vg1019669777 NA 3.22E-12 mr1879_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
vg1019669777 NA 3.63E-09 mr1879_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