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Detailed information for vg1021046076:

Variant ID: vg1021046076 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 21046076
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTCAGAGAGGAAAGCCATGGAGTAAGGTTGATGTGCCCGCCGTTGTGATTGATGGCATCCTTAGATCAGATCTGATGGTGTCGCCACAATCAACCCTTAT[C/T]
CGATACCTAAGGGACATTGTTTCCAAAGGAAGATTAAGTGAGCGAAGCCATAGAGCAAGTTTGATGTGCCCACCGCCACGACTAGATCCCCTATCTGCCG

Reverse complement sequence

CGGCAGATAGGGGATCTAGTCGTGGCGGTGGGCACATCAAACTTGCTCTATGGCTTCGCTCACTTAATCTTCCTTTGGAAACAATGTCCCTTAGGTATCG[G/A]
ATAAGGGTTGATTGTGGCGACACCATCAGATCTGATCTAAGGATGCCATCAATCACAACGGCGGGCACATCAACCTTACTCCATGGCTTTCCTCTCTGAC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.40% 0.90% 0.72% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 95.10% 2.60% 2.25% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 92.30% 4.20% 3.52% 0.00% NA
Tropical Japonica  504 99.60% 0.20% 0.20% 0.00% NA
Japonica Intermediate  241 94.60% 2.90% 2.49% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg1021046076 C -> T LOC_Os10g39434.1 upstream_gene_variant ; 4772.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021046076 C -> T LOC_Os10g39440.1 upstream_gene_variant ; 2195.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021046076 C -> T LOC_Os10g39440.2 upstream_gene_variant ; 2195.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021046076 C -> T LOC_Os10g39434-LOC_Os10g39440 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1021046076 NA 9.16E-08 mr1280 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
vg1021046076 NA 6.85E-06 mr1788 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
vg1021046076 NA 8.62E-09 mr1807 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
vg1021046076 NA 4.32E-06 mr1921 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
vg1021046076 NA 1.29E-06 mr1807_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