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Detailed information for vg1010405672:

Variant ID: vg1010405672 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 10405672
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGATTTCGCTTCTACCCCGGGTGAATCGCACCAATTTTTGCCGTGTGTTTGAATTAAAGCTTGTCAGTAACTTTCCCTCTCACAATTTAAACTGGGCGCC[A/G]
CCGAGCCGACCATTTTACCCCTCGCCGCCGCGGCACATCGAACATGGGAAGACGCCAGCTCACCACCGCTCGTTTTCATCCCTGGTCAAACATTTCAGTC

Reverse complement sequence

GACTGAAATGTTTGACCAGGGATGAAAACGAGCGGTGGTGAGCTGGCGTCTTCCCATGTTCGATGTGCCGCGGCGGCGAGGGGTAAAATGGTCGGCTCGG[T/C]
GGCGCCCAGTTTAAATTGTGAGAGGGAAAGTTACTGACAAGCTTTAATTCAAACACACGGCAAAAATTGGTGCGATTCACCCGGGGTAGAAGCGAAATCG

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 95.20% 4.70% 0.08% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 85.80% 14.00% 0.26% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 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 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 81.10% 18.60% 0.26% 0.00% NA
Tropical Japonica  504 97.00% 3.00% 0.00% 0.00% NA
Japonica Intermediate  241 77.20% 22.00% 0.83% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 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
vg1010405672 A -> G LOC_Os10g20610-LOC_Os10g20630 intergenic_region ; MODIFIER silent_mutation Average:56.573; most accessible tissue: Zhenshan97 young leaf, score: 82.31 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1010405672 NA 1.30E-06 mr1164_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
vg1010405672 NA 9.24E-08 mr1296_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
vg1010405672 NA 6.75E-06 mr1358_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
vg1010405672 NA 2.17E-06 mr1865_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