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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0523132370:

Variant ID: vg0523132370 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 23132370
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCCCCGCCCCCCGACCTTCTGGCGCTGCTATCTCCATCCCCGCCATCCAGTGTTGCCCCCTCTGCCTCAGCTCCACGGGTTGTCGTAGAGAGAAGCCGCC[G/A]
CCGTCGCCAGCCTCTACGTGGTCGTCATCACGTGGGAAGATGAACGAGAGAAGAGGAAGAAGGGAGAGAAGAGGAAGAGGGAGAGAAAGAGGAGGAAGAA

Reverse complement sequence

TTCTTCCTCCTCTTTCTCTCCCTCTTCCTCTTCTCTCCCTTCTTCCTCTTCTCTCGTTCATCTTCCCACGTGATGACGACCACGTAGAGGCTGGCGACGG[C/T]
GGCGGCTTCTCTCTACGACAACCCGTGGAGCTGAGGCAGAGGGGGCAACACTGGATGGCGGGGATGGAGATAGCAGCGCCAGAAGGTCGGGGGGCGGGGG

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 95.50% 3.60% 0.89% 0.00% NA
All Indica  2759 99.80% 0.20% 0.04% 0.00% NA
All Japonica  1512 97.00% 0.50% 2.58% 0.00% NA
Aus  269 55.80% 44.20% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.40% 0.13% 0.00% NA
Temperate Japonica  767 94.80% 0.90% 4.30% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 0.00% 2.49% 0.00% NA
VI/Aromatic  96 62.50% 36.50% 1.04% 0.00% NA
Intermediate  90 93.30% 5.60% 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
vg0523132370 G -> A LOC_Os05g39440.1 synonymous_variant ; p.Gly49Gly; LOW synonymous_codon Average:66.534; most accessible tissue: Zhenshan97 flag leaf, score: 81.796 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0523132370 NA 4.91E-06 mr1633 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
vg0523132370 NA 5.51E-09 mr1057_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
vg0523132370 NA 4.55E-10 mr1126_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
vg0523132370 NA 3.04E-06 mr1127_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
vg0523132370 NA 2.97E-10 mr1166_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
vg0523132370 3.83E-06 2.09E-09 mr1465_2 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
vg0523132370 NA 7.25E-10 mr1567_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
vg0523132370 NA 1.60E-14 mr1612_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