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Detailed information for vg1013687229:

Variant ID: vg1013687229 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 13687229
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACCTGCACCTCCCAAGACAAGGTCTTGCCAAGCTCCACCGCCTGCCCGCACAAGGGCAACGAAGAAGGCGAAAGTTGACGCCACCAAAAACAAGGAGCC[G/A]
CCGTACGATTGCAGTCAAGAGGAGCTTGATACTTATGTGGCAGGAGAAGTGAAGAGGAAATTCAAGCCTCGGAGTCCTGAAAAGAAGATACCTATTGACC

Reverse complement sequence

GGTCAATAGGTATCTTCTTTTCAGGACTCCGAGGCTTGAATTTCCTCTTCACTTCTCCTGCCACATAAGTATCAAGCTCCTCTTGACTGCAATCGTACGG[C/T]
GGCTCCTTGTTTTTGGTGGCGTCAACTTTCGCCTTCTTCGTTGCCCTTGTGCGGGCAGGCGGTGGAGCTTGGCAAGACCTTGTCTTGGGAGGTGCAGGTG

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 59.80% 29.30% 10.90% 0.00% NA
All Indica  2759 33.00% 48.90% 18.16% 0.00% NA
All Japonica  1512 99.50% 0.30% 0.20% 0.00% NA
Aus  269 92.60% 5.90% 1.49% 0.00% NA
Indica I  595 33.10% 55.80% 11.09% 0.00% NA
Indica II  465 14.00% 61.70% 24.30% 0.00% NA
Indica III  913 40.60% 39.30% 20.04% 0.00% NA
Indica Intermediate  786 35.20% 47.10% 17.68% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 0.40% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 75.60% 16.70% 7.78% 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
vg1013687229 G -> A LOC_Os10g26370.1 synonymous_variant ; p.Pro1550Pro; LOW synonymous_codon Average:24.205; most accessible tissue: Zhenshan97 flag leaf, score: 33.231 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1013687229 NA 4.51E-07 mr1533 Ind_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
vg1013687229 7.54E-06 1.41E-08 mr1980 Ind_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
vg1013687229 3.46E-07 NA mr1533_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
vg1013687229 5.45E-08 8.87E-13 mr1533_2 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
vg1013687229 1.70E-06 NA mr1860_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
vg1013687229 NA 1.08E-06 mr1980_2 Ind_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