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Detailed information for vg0233347033:

Variant ID: vg0233347033 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 33347033
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGCCGCGTCCTCCTCGGCGGTGAGGTTGCACACGACGAACCGGACGTGGACCACGGCGCGGGCGGGCGCCGGCTGGAGCGCGTAGGCGAGGCGGACCAG[C/A]
GCGCGCCGCTCGTACTTGTCGGCGCGGGTGAGCACGCCGAGGAGCACGCGGATGTCCGGGGCCGCCTTCGCCACCGCGTCGGCCGCCGTCGCCGGCGCGC

Reverse complement sequence

GCGCGCCGGCGACGGCGGCCGACGCGGTGGCGAAGGCGGCCCCGGACATCCGCGTGCTCCTCGGCGTGCTCACCCGCGCCGACAAGTACGAGCGGCGCGC[G/T]
CTGGTCCGCCTCGCCTACGCGCTCCAGCCGGCGCCCGCCCGCGCCGTGGTCCACGTCCGGTTCGTCGTGTGCAACCTCACCGCCGAGGAGGACGCGGCGC

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 94.10% 5.90% 0.02% 0.00% NA
All Indica  2759 97.50% 2.50% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 27.90% 71.70% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 96.40% 3.60% 0.00% 0.00% NA
Indica Intermediate  786 95.90% 4.10% 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 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0233347033 C -> A LOC_Os02g54420.1 synonymous_variant ; p.Ala75Ala; LOW synonymous_codon Average:73.496; most accessible tissue: Zhenshan97 young leaf, score: 81.353 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0233347033 NA 5.40E-06 mr1263_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