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Detailed information for vg1010554538:

Variant ID: vg1010554538 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 10554538
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGAACACGAGGGAAAGGCGTGATTCCCTGGAAGATTAGATTCAAGGAGGACATCCACACGTACAGGAGTTGGATGAGGAGTAAGAGAGATATCGAGGCGA[A/G]
GATTGCAAATCTTGAGTACAGGGTATCGAGCTACGAGCTCAGCATGCAAGAGGAGGTGGCAAGGAAGGTGGATGAATGCATGGCCGCACATCGGTCCCAG

Reverse complement sequence

CTGGGACCGATGTGCGGCCATGCATTCATCCACCTTCCTTGCCACCTCCTCTTGCATGCTGAGCTCGTAGCTCGATACCCTGTACTCAAGATTTGCAATC[T/C]
TCGCCTCGATATCTCTCTTACTCCTCATCCAACTCCTGTACGTGTGGATGTCCTCCTTGAATCTAATCTTCCAGGGAATCACGCCTTTCCCTCGTGTTCG

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 23.00% 0.80% 4.44% 71.69% NA
All Indica  2759 2.90% 1.40% 5.18% 90.50% NA
All Japonica  1512 62.80% 0.00% 2.65% 34.52% NA
Aus  269 3.70% 0.00% 5.95% 90.33% NA
Indica I  595 1.80% 3.90% 3.19% 91.09% NA
Indica II  465 1.90% 1.10% 3.23% 93.76% NA
Indica III  913 3.50% 0.00% 6.24% 90.25% NA
Indica Intermediate  786 3.40% 1.50% 6.62% 88.42% NA
Temperate Japonica  767 77.10% 0.00% 4.56% 18.38% NA
Tropical Japonica  504 48.40% 0.00% 0.20% 51.39% NA
Japonica Intermediate  241 47.70% 0.00% 1.66% 50.62% NA
VI/Aromatic  96 16.70% 0.00% 8.33% 75.00% NA
Intermediate  90 36.70% 0.00% 3.33% 60.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1010554538 A -> G LOC_Os10g20810.1 missense_variant ; p.Lys150Arg; MODERATE nonsynonymous_codon ; K150R Average:9.744; most accessible tissue: Callus, score: 30.695 unknown unknown DELETERIOUS 0.00
vg1010554538 A -> DEL LOC_Os10g20810.1 N frameshift_variant Average:9.744; most accessible tissue: Callus, score: 30.695 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1010554538 NA 1.03E-07 mr1162 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
vg1010554538 8.37E-06 8.37E-06 mr1551 Ind_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
vg1010554538 9.66E-07 NA mr1679 Ind_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
vg1010554538 2.69E-07 1.75E-07 mr1768 Ind_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
vg1010554538 NA 1.43E-07 mr1837_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