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Detailed information for vg1227091155:

Variant ID: vg1227091155 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 27091155
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATATAATTAGGGATTGGCTGGCTGGGCGGATTTGGTTGGAATTAAGTAGTGGATCCTACGAAGAAGCCCACGGTGAGAAGATGGAAGGAGGATGACTGCG[C/A]
TTTTAAAGTAGTAGAGAAAACTAGTTGTTACTAGATTTGTGGTTGAGTCATTTAGTGAATAAATCAGTCGAAATGCAGTGTGAAAATTGTTGACAGGTAA

Reverse complement sequence

TTACCTGTCAACAATTTTCACACTGCATTTCGACTGATTTATTCACTAAATGACTCAACCACAAATCTAGTAACAACTAGTTTTCTCTACTACTTTAAAA[G/T]
CGCAGTCATCCTCCTTCCATCTTCTCACCGTGGGCTTCTTCGTAGGATCCACTACTTAATTCCAACCAAATCCGCCCAGCCAGCCAATCCCTAATTATAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.60% 1.80% 0.66% 0.99% NA
All Indica  2759 98.80% 0.00% 0.14% 1.01% NA
All Japonica  1512 92.70% 5.40% 1.79% 0.07% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.00% 0.67% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 97.30% 0.00% 0.00% 2.74% NA
Indica Intermediate  786 99.50% 0.10% 0.00% 0.38% NA
Temperate Japonica  767 90.70% 6.00% 3.26% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 85.50% 13.30% 0.83% 0.41% NA
VI/Aromatic  96 83.30% 0.00% 0.00% 16.67% NA
Intermediate  90 96.70% 1.10% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1227091155 C -> DEL N N silent_mutation Average:51.056; most accessible tissue: Zhenshan97 root, score: 87.373 N N N N
vg1227091155 C -> A LOC_Os12g43620.1 downstream_gene_variant ; 1012.0bp to feature; MODIFIER silent_mutation Average:51.056; most accessible tissue: Zhenshan97 root, score: 87.373 N N N N
vg1227091155 C -> A LOC_Os12g43630.1 downstream_gene_variant ; 3492.0bp to feature; MODIFIER silent_mutation Average:51.056; most accessible tissue: Zhenshan97 root, score: 87.373 N N N N
vg1227091155 C -> A LOC_Os12g43630.2 downstream_gene_variant ; 3492.0bp to feature; MODIFIER silent_mutation Average:51.056; most accessible tissue: Zhenshan97 root, score: 87.373 N N N N
vg1227091155 C -> A LOC_Os12g43620-LOC_Os12g43630 intergenic_region ; MODIFIER silent_mutation Average:51.056; most accessible tissue: Zhenshan97 root, score: 87.373 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1227091155 4.64E-08 6.63E-06 mr1613_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
vg1227091155 7.23E-06 NA mr1619_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
vg1227091155 9.63E-09 4.93E-06 mr1962_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