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Detailed information for vg0522746957:

Variant ID: vg0522746957 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 22746957
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGTCGGTGGCCGCGGCGAGCTCGCGGAACGCGAACGCCTGCCCGGCGATGGCGAGCCCCGCCGAGGCGTCCTCGGATGGCTTGGGGGCCTGATCTGCAT[G/C]
GAGAGACCGCGCGCGCGCATTAGCCAATTGGAAGCCATGGTCAATGTGGGATCATCGAACTAGCCAAGAAATCGGATCGAGGAAGCTATCACTCACCGGG

Reverse complement sequence

CCCGGTGAGTGATAGCTTCCTCGATCCGATTTCTTGGCTAGTTCGATGATCCCACATTGACCATGGCTTCCAATTGGCTAATGCGCGCGCGCGGTCTCTC[C/G]
ATGCAGATCAGGCCCCCAAGCCATCCGAGGACGCCTCGGCGGGGCTCGCCATCGCCGGGCAGGCGTTCGCGTTCCGCGAGCTCGCCGCGGCCACCGACCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.60% 5.40% 0.00% 0.00% NA
All Indica  2759 90.90% 9.10% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 67.90% 32.10% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 98.70% 1.30% 0.00% 0.00% NA
Indica Intermediate  786 94.70% 5.30% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0522746957 G -> C LOC_Os05g38770.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:72.32; most accessible tissue: Zhenshan97 flower, score: 84.964 N N N N
vg0522746957 G -> C LOC_Os05g38760.1 upstream_gene_variant ; 2505.0bp to feature; MODIFIER silent_mutation Average:72.32; most accessible tissue: Zhenshan97 flower, score: 84.964 N N N N
vg0522746957 G -> C LOC_Os05g38780.1 upstream_gene_variant ; 4586.0bp to feature; MODIFIER silent_mutation Average:72.32; most accessible tissue: Zhenshan97 flower, score: 84.964 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0522746957 NA 6.52E-06 mr1547 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