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Detailed information for vg1003806408:

Variant ID: vg1003806408 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3806408
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCTACCTCGGTCAAAGCGTCCTCCCACCGGTCAAACCCGCCCACCACTTTGCTGCTCTCGTATTGTAGGAATCGTGCAGTAACAGGACGGTCATCCTGCA[G/A,T]
TAACAAGACAGCATTATCGCAGTAACAACGTCAAAAAGTAGCCATGATGGATCTAGTTTCGTTAAGTGTTTTTTTATGAACTTTATGGTGCAAACGGATT

Reverse complement sequence

AATCCGTTTGCACCATAAAGTTCATAAAAAAACACTTAACGAAACTAGATCCATCATGGCTACTTTTTGACGTTGTTACTGCGATAATGCTGTCTTGTTA[C/T,A]
TGCAGGATGACCGTCCTGTTACTGCACGATTCCTACAATACGAGAGCAGCAAAGTGGTGGGCGGGTTTGACCGGTGGGAGGACGCTTTGACCGAGGTAGG

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 97.40% 1.00% 0.85% 0.00% T: 0.76%
All Indica  2759 99.80% 0.10% 0.11% 0.00% NA
All Japonica  1512 92.20% 3.00% 2.45% 0.00% T: 2.38%
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.10% 0.25% 0.00% NA
Temperate Japonica  767 86.00% 4.40% 4.82% 0.00% T: 4.69%
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 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
vg1003806408 G -> T LOC_Os10g07229.1 upstream_gene_variant ; 2390.0bp to feature; MODIFIER silent_mutation Average:37.854; most accessible tissue: Minghui63 root, score: 64.607 N N N N
vg1003806408 G -> T LOC_Os10g07248.1 upstream_gene_variant ; 4800.0bp to feature; MODIFIER silent_mutation Average:37.854; most accessible tissue: Minghui63 root, score: 64.607 N N N N
vg1003806408 G -> T LOC_Os10g07229-LOC_Os10g07248 intergenic_region ; MODIFIER silent_mutation Average:37.854; most accessible tissue: Minghui63 root, score: 64.607 N N N N
vg1003806408 G -> A LOC_Os10g07229.1 upstream_gene_variant ; 2390.0bp to feature; MODIFIER silent_mutation Average:37.854; most accessible tissue: Minghui63 root, score: 64.607 N N N N
vg1003806408 G -> A LOC_Os10g07248.1 upstream_gene_variant ; 4800.0bp to feature; MODIFIER silent_mutation Average:37.854; most accessible tissue: Minghui63 root, score: 64.607 N N N N
vg1003806408 G -> A LOC_Os10g07229-LOC_Os10g07248 intergenic_region ; MODIFIER silent_mutation Average:37.854; most accessible tissue: Minghui63 root, score: 64.607 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003806408 2.10E-07 6.96E-06 mr1124 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
vg1003806408 2.78E-08 2.78E-08 mr1855 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