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Detailed information for vg1009899148:

Variant ID: vg1009899148 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 9899148
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAACATCGATGACTGTGGACAATTATCAACATATTTTTAGTTAGGAAAAAGTACGAATTACCCCCCTGAACTATCGCGGTCGTCCAAATTACCCCCCTGA[G/A]
CCACAAAACCGGACATTCTTCACCCCCAACTATGCAAACCGGACGAATTACCCCCCTCGACCCAATCCGCGGTGGTTTTGGTCTACGTGGCGTACGCGTG

Reverse complement sequence

CACGCGTACGCCACGTAGACCAAAACCACCGCGGATTGGGTCGAGGGGGGTAATTCGTCCGGTTTGCATAGTTGGGGGTGAAGAATGTCCGGTTTTGTGG[C/T]
TCAGGGGGGTAATTTGGACGACCGCGATAGTTCAGGGGGGTAATTCGTACTTTTTCCTAACTAAAAATATGTTGATAATTGTCCACAGTCATCGATGTTA

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 75.90% 22.90% 1.18% 0.00% NA
All Indica  2759 98.80% 1.20% 0.00% 0.00% NA
All Japonica  1512 28.80% 67.60% 3.57% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 98.10% 1.90% 0.00% 0.00% NA
Indica Intermediate  786 99.00% 1.00% 0.00% 0.00% NA
Temperate Japonica  767 9.80% 83.20% 7.04% 0.00% NA
Tropical Japonica  504 54.60% 45.40% 0.00% 0.00% NA
Japonica Intermediate  241 35.70% 64.30% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 67.80% 30.00% 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
vg1009899148 G -> A LOC_Os10g19850.1 upstream_gene_variant ; 1851.0bp to feature; MODIFIER silent_mutation Average:63.962; most accessible tissue: Zhenshan97 flower, score: 78.5 N N N N
vg1009899148 G -> A LOC_Os10g19850-LOC_Os10g19860 intergenic_region ; MODIFIER silent_mutation Average:63.962; most accessible tissue: Zhenshan97 flower, score: 78.5 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1009899148 NA 1.19E-07 mr1495 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
vg1009899148 NA 1.20E-06 mr1622 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
vg1009899148 2.91E-11 2.18E-24 mr1768 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
vg1009899148 NA 2.75E-07 mr1815 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
vg1009899148 NA 6.16E-06 mr1118_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
vg1009899148 NA 1.58E-08 mr1495_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
vg1009899148 1.23E-06 5.22E-32 mr1768_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