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Detailed information for vg0617763556:

Variant ID: vg0617763556 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 17763556
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCTGAAGTTGATCCACGTTCTGTATCAGTACTGGTCGAAGTAGTAATCTCCAGAGGACCATCCTGATCAGCATCAACAGTACCGGAACCCGACGGACCT[G/A]
GCCGGTCTGACCGCTCCTCCTGAGGCGGTCTGACCGGCCGAGCCGACCTCGTCATCGTCGTTGTCGTCGCTCTCATCTTCAAAAATACGACCATCCTCCC

Reverse complement sequence

GGGAGGATGGTCGTATTTTTGAAGATGAGAGCGACGACAACGACGATGACGAGGTCGGCTCGGCCGGTCAGACCGCCTCAGGAGGAGCGGTCAGACCGGC[C/T]
AGGTCCGTCGGGTTCCGGTACTGTTGATGCTGATCAGGATGGTCCTCTGGAGATTACTACTTCGACCAGTACTGATACAGAACGTGGATCAACTTCAGAA

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 93.80% 6.10% 0.04% 0.00% NA
All Indica  2759 90.70% 9.20% 0.04% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 90.70% 9.30% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 95.50% 4.50% 0.00% 0.00% NA
Indica III  913 83.90% 16.10% 0.00% 0.00% NA
Indica Intermediate  786 89.60% 10.30% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 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 94.40% 4.40% 1.11% 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
vg0617763556 G -> A LOC_Os06g30670.1 splice_region_variant&synonymous_variant ; p.Ala640Ala; LOW synonymous_codon Average:43.483; most accessible tissue: Minghui63 young leaf, score: 71.254 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0617763556 2.40E-06 2.40E-06 mr1808 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