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Detailed information for vg1008369782:

Variant ID: vg1008369782 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 8369782
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTGCACCTCCCAAGACAAGGTCTCGCCAAGCTCCACCGCCTGCCCGCACAAGGGCAACGAAGAAGGCGAAAGTTGACGCCACCAAAAACAAGGAGCCGCC[G/A]
TACGATTGCAGTCAAGAGGAGCTTGATGCTTATGTGGCAGGAGAAGTGAAGAGGCAACTCAAGCCTCGGAGTCCTGAAAAGAAGATACCTATTGACCCGA

Reverse complement sequence

TCGGGTCAATAGGTATCTTCTTTTCAGGACTCCGAGGCTTGAGTTGCCTCTTCACTTCTCCTGCCACATAAGCATCAAGCTCCTCTTGACTGCAATCGTA[C/T]
GGCGGCTCCTTGTTTTTGGTGGCGTCAACTTTCGCCTTCTTCGTTGCCCTTGTGCGGGCAGGCGGTGGAGCTTGGCGAGACCTTGTCTTGGGAGGTGCAG

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 93.40% 6.10% 0.23% 0.30% NA
All Indica  2759 99.90% 0.00% 0.00% 0.07% NA
All Japonica  1512 80.20% 18.50% 0.66% 0.66% NA
Aus  269 100.00% 0.00% 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% 0.10% 0.00% 0.11% NA
Indica Intermediate  786 99.90% 0.00% 0.00% 0.13% NA
Temperate Japonica  767 65.20% 34.20% 0.52% 0.13% NA
Tropical Japonica  504 97.60% 1.80% 0.40% 0.20% NA
Japonica Intermediate  241 91.30% 3.70% 1.66% 3.32% NA
VI/Aromatic  96 95.80% 3.10% 1.04% 0.00% NA
Intermediate  90 94.40% 3.30% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1008369782 G -> A LOC_Os10g16800.1 intron_variant ; MODIFIER silent_mutation Average:57.895; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 N N N N
vg1008369782 G -> DEL N N silent_mutation Average:57.895; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1008369782 7.84E-08 NA mr1300 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
vg1008369782 NA 9.16E-07 mr1300 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
vg1008369782 8.80E-07 NA mr1310 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
vg1008369782 NA 1.23E-06 mr1310 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
vg1008369782 3.48E-07 NA mr1926 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
vg1008369782 3.46E-08 NA mr1768_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