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Detailed information for vg1007906158:

Variant ID: vg1007906158 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 7906158
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGAGGATTAGGCTTCATCCGAGCCGTCGAGGATGCCTGTGGAGTGGTGTTCCCATTGCAGTCCAAGTCAAGGCTTAGCTCCAGTTATCTTTTAATTTTCC[G/A]
CTGCATTTGTGTAATGTCACGCCCAGAAATTCACTAGTAATTTCCGAACTTATTTGTGCATTAAATCCTCGTCCAGGAATCAGCCGAGGTACACAAACTG

Reverse complement sequence

CAGTTTGTGTACCTCGGCTGATTCCTGGACGAGGATTTAATGCACAAATAAGTTCGGAAATTACTAGTGAATTTCTGGGCGTGACATTACACAAATGCAG[C/T]
GGAAAATTAAAAGATAACTGGAGCTAAGCCTTGACTTGGACTGCAATGGGAACACCACTCCACAGGCATCCTCGACGGCTCGGATGAAGCCTAATCCTCG

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 28.60% 1.70% 3.83% 65.95% NA
All Indica  2759 8.00% 0.00% 4.86% 87.10% NA
All Japonica  1512 68.10% 4.90% 2.45% 24.60% NA
Aus  269 1.50% 0.00% 0.74% 97.77% NA
Indica I  595 7.60% 0.00% 2.69% 89.75% NA
Indica II  465 8.40% 0.20% 4.95% 86.45% NA
Indica III  913 9.10% 0.00% 6.79% 84.12% NA
Indica Intermediate  786 6.90% 0.00% 4.20% 88.93% NA
Temperate Japonica  767 88.80% 4.40% 0.91% 5.87% NA
Tropical Japonica  504 39.30% 6.50% 4.56% 49.60% NA
Japonica Intermediate  241 62.20% 2.90% 2.90% 31.95% NA
VI/Aromatic  96 56.20% 0.00% 5.21% 38.54% NA
Intermediate  90 46.70% 3.30% 3.33% 46.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1007906158 G -> A LOC_Os10g15079-LOC_Os10g15100 intergenic_region ; MODIFIER silent_mutation Average:13.443; most accessible tissue: Zhenshan97 root, score: 22.162 N N N N
vg1007906158 G -> DEL N N silent_mutation Average:13.443; most accessible tissue: Zhenshan97 root, score: 22.162 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1007906158 NA 3.50E-06 mr1232_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
vg1007906158 1.24E-06 8.13E-09 mr1398_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
vg1007906158 NA 6.86E-06 mr1415_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
vg1007906158 3.88E-06 3.88E-06 mr1424_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
vg1007906158 NA 6.25E-06 mr1510_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
vg1007906158 NA 5.81E-06 mr1557_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
vg1007906158 NA 2.34E-07 mr1558_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
vg1007906158 2.09E-06 2.09E-06 mr1562_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
vg1007906158 NA 1.15E-08 mr1676_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
vg1007906158 NA 7.79E-06 mr1944_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