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Detailed information for vg0807832561:

Variant ID: vg0807832561 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 7832561
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTGTGAGCTCGTTGATGTACTCCTCCATAGCTTTACGATCTTCTCCTTCGAAGTCTTCCAATGCGACCGGTATCACATTAGATGGCTCCACCTCCGTCTT[A/G]
GATAGCGGCTTCGTCATGGCGAAGTCAAAGTTGAGTTGACGATGAACGGATCTCCTCCCCAGCAGAGTCGCCAAAAATCGTGTTGGCAACTTTTTGTGAC

Reverse complement sequence

GTCACAAAAAGTTGCCAACACGATTTTTGGCGACTCTGCTGGGGAGGAGATCCGTTCATCGTCAACTCAACTTTGACTTCGCCATGACGAAGCCGCTATC[T/C]
AAGACGGAGGTGGAGCCATCTAATGTGATACCGGTCGCATTGGAAGACTTCGAAGGAGAAGATCGTAAAGCTATGGAGGAGTACATCAACGAGCTCACAC

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 69.40% 28.60% 1.95% 0.00% NA
All Indica  2759 95.80% 0.90% 3.30% 0.00% NA
All Japonica  1512 14.40% 85.60% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 99.30% 0.50% 0.17% 0.00% NA
Indica II  465 96.10% 2.20% 1.72% 0.00% NA
Indica III  913 91.50% 0.40% 8.11% 0.00% NA
Indica Intermediate  786 98.00% 1.00% 1.02% 0.00% NA
Temperate Japonica  767 7.00% 93.00% 0.00% 0.00% NA
Tropical Japonica  504 20.80% 79.20% 0.00% 0.00% NA
Japonica Intermediate  241 24.10% 75.90% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 70.00% 28.90% 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
vg0807832561 A -> G LOC_Os08g13170.1 synonymous_variant ; p.Ser6Ser; LOW synonymous_codon Average:59.512; most accessible tissue: Minghui63 young leaf, score: 85.236 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0807832561 NA 2.32E-07 mr1030_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
vg0807832561 9.01E-06 NA mr1071_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
vg0807832561 NA 3.44E-15 mr1162_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
vg0807832561 6.75E-06 NA mr1203_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
vg0807832561 NA 1.56E-23 mr1350_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
vg0807832561 NA 3.56E-34 mr1448_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
vg0807832561 NA 1.21E-44 mr1486_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
vg0807832561 2.76E-07 2.76E-07 mr1542_2 Jap_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
vg0807832561 NA 7.24E-26 mr1588_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
vg0807832561 NA 8.83E-26 mr1617_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
vg0807832561 NA 8.81E-21 mr1968_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