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Detailed information for vg1204623407:

Variant ID: vg1204623407 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 4623407
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.83, G: 0.18, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


AACGAAAAGGTAATAATTTCCTGGGTGTGAGCCGACGCGGCAAGACGAATCTGAACCTTCTCACCTTGCACCGATATATGGATCCTTCCCCTATCCAGGC[T/G]
TCGCACATCAAATTCGGGGGATGTACAGGCTAGGGTCTGCATGCATGCTGGTATCTACAGAATCTTCTTCGTAGTGAGCATGGCAATGTAACAAACAGAA

Reverse complement sequence

TTCTGTTTGTTACATTGCCATGCTCACTACGAAGAAGATTCTGTAGATACCAGCATGCATGCAGACCCTAGCCTGTACATCCCCCGAATTTGATGTGCGA[A/C]
GCCTGGATAGGGGAAGGATCCATATATCGGTGCAAGGTGAGAAGGTTCAGATTCGTCTTGCCGCGTCGGCTCACACCCAGGAAATTATTACCTTTTCGTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 36.20% 10.40% 0.85% 52.60% NA
All Indica  2759 4.50% 5.40% 1.38% 88.76% NA
All Japonica  1512 87.50% 11.80% 0.07% 0.66% NA
Aus  269 42.40% 56.90% 0.00% 0.74% NA
Indica I  595 2.90% 11.80% 0.84% 84.54% NA
Indica II  465 6.20% 0.60% 1.51% 91.61% NA
Indica III  913 2.70% 2.00% 1.31% 93.98% NA
Indica Intermediate  786 6.60% 7.40% 1.78% 84.22% NA
Temperate Japonica  767 95.00% 4.20% 0.13% 0.65% NA
Tropical Japonica  504 91.30% 7.90% 0.00% 0.79% NA
Japonica Intermediate  241 55.60% 44.00% 0.00% 0.41% NA
VI/Aromatic  96 93.80% 4.20% 1.04% 1.04% NA
Intermediate  90 65.60% 7.80% 0.00% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1204623407 T -> DEL N N silent_mutation Average:13.057; most accessible tissue: Callus, score: 83.017 N N N N
vg1204623407 T -> G LOC_Os12g08890-LOC_Os12g08900 intergenic_region ; MODIFIER silent_mutation Average:13.057; most accessible tissue: Callus, score: 83.017 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1204623407 NA 3.24E-06 mr1117 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
vg1204623407 NA 1.23E-06 mr1123 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
vg1204623407 NA 5.29E-07 mr1242 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
vg1204623407 5.26E-07 NA mr1679 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
vg1204623407 NA 8.28E-09 mr1679 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
vg1204623407 5.34E-07 8.38E-10 mr1691 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
vg1204623407 1.21E-07 4.69E-14 mr1693 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
vg1204623407 6.55E-06 3.69E-08 mr1720 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
vg1204623407 NA 2.25E-06 mr1042_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
vg1204623407 NA 1.45E-06 mr1117_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
vg1204623407 NA 5.93E-06 mr1119_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
vg1204623407 NA 5.81E-06 mr1123_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
vg1204623407 NA 4.08E-07 mr1496_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
vg1204623407 NA 1.54E-06 mr1594_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
vg1204623407 NA 5.66E-07 mr1679_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
vg1204623407 6.59E-06 1.18E-09 mr1691_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
vg1204623407 NA 5.73E-08 mr1720_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