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Detailed information for vg0222636576:

Variant ID: vg0222636576 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22636576
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTATCATTTAGTTTATTATGACTTGATTCGTCATCAAATGTTCTTTAAGCATGACATAAATATTTTCATATTTGCATAAAAGTTTTGAATAAAACGAAT[G/A]
GTCAAACGTTAGTTGAAAAGTCAACGGCGTTGTACATTAGGATACGGAGGGAGTACGATATTTATGCATCCACGCATGCATGCAGAGGCGGCCAACTCGC

Reverse complement sequence

GCGAGTTGGCCGCCTCTGCATGCATGCGTGGATGCATAAATATCGTACTCCCTCCGTATCCTAATGTACAACGCCGTTGACTTTTCAACTAACGTTTGAC[C/T]
ATTCGTTTTATTCAAAACTTTTATGCAAATATGAAAATATTTATGTCATGCTTAAAGAACATTTGATGACGAATCAAGTCATAATAAACTAAATGATAAT

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 79.60% 20.40% 0.08% 0.00% NA
All Indica  2759 96.30% 3.70% 0.04% 0.00% NA
All Japonica  1512 57.70% 42.20% 0.13% 0.00% NA
Aus  269 32.70% 67.30% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 93.30% 6.50% 0.22% 0.00% NA
Indica III  913 98.00% 2.00% 0.00% 0.00% NA
Indica Intermediate  786 94.00% 6.00% 0.00% 0.00% NA
Temperate Japonica  767 81.20% 18.80% 0.00% 0.00% NA
Tropical Japonica  504 25.80% 73.80% 0.40% 0.00% NA
Japonica Intermediate  241 49.40% 50.60% 0.00% 0.00% NA
VI/Aromatic  96 80.20% 19.80% 0.00% 0.00% NA
Intermediate  90 73.30% 25.60% 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
vg0222636576 G -> A LOC_Os02g37510.1 downstream_gene_variant ; 1706.0bp to feature; MODIFIER silent_mutation Average:55.54; most accessible tissue: Minghui63 root, score: 75.485 N N N N
vg0222636576 G -> A LOC_Os02g37500.1 intron_variant ; MODIFIER silent_mutation Average:55.54; most accessible tissue: Minghui63 root, score: 75.485 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222636576 4.65E-06 NA mr1117 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
vg0222636576 9.93E-06 NA mr1118 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
vg0222636576 NA 5.26E-06 mr1518 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
vg0222636576 5.37E-06 NA mr1113_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
vg0222636576 2.09E-06 NA mr1114_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
vg0222636576 7.33E-08 NA mr1117_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
vg0222636576 2.21E-07 NA mr1118_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
vg0222636576 2.04E-07 NA mr1119_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
vg0222636576 9.97E-06 NA mr1120_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
vg0222636576 8.96E-07 NA mr1123_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
vg0222636576 3.18E-06 NA mr1240_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
vg0222636576 9.17E-08 NA mr1242_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
vg0222636576 5.46E-09 NA mr1496_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