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Detailed information for vg0312772189:

Variant ID: vg0312772189 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 12772189
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATAATATGGGAGAAGATAATGAGTCATACTTGTATGACACTTAAGATGCTAATTAGTAGTGGGTGATGAAATGACATACTTGTATGTTGAGTTTTAGTTT[C/T]
TAATAGGTGTTAGTGGGTGCCAACTACTCCCATCCGTTTCTAAATATTTGACGCCGTTGAATTTTTTAAATATGTTTGACCATTTGTCTTATTCAAAAAA

Reverse complement sequence

TTTTTTGAATAAGACAAATGGTCAAACATATTTAAAAAATTCAACGGCGTCAAATATTTAGAAACGGATGGGAGTAGTTGGCACCCACTAACACCTATTA[G/A]
AAACTAAAACTCAACATACAAGTATGTCATTTCATCACCCACTACTAATTAGCATCTTAAGTGTCATACAAGTATGACTCATTATCTTCTCCCATATTAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.90% 3.60% 0.47% 0.00% NA
All Indica  2759 99.70% 0.10% 0.18% 0.00% NA
All Japonica  1512 88.40% 10.70% 0.93% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 99.50% 0.00% 0.50% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.30% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 68.70% 28.80% 2.58% 0.00% NA
Japonica Intermediate  241 92.90% 6.60% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 6.70% 2.22% 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
vg0312772189 C -> T LOC_Os03g22270.1 upstream_gene_variant ; 3309.0bp to feature; MODIFIER silent_mutation Average:57.882; most accessible tissue: Zhenshan97 flag leaf, score: 77.738 N N N N
vg0312772189 C -> T LOC_Os03g22290.1 upstream_gene_variant ; 3800.0bp to feature; MODIFIER silent_mutation Average:57.882; most accessible tissue: Zhenshan97 flag leaf, score: 77.738 N N N N
vg0312772189 C -> T LOC_Os03g22300.1 upstream_gene_variant ; 4733.0bp to feature; MODIFIER silent_mutation Average:57.882; most accessible tissue: Zhenshan97 flag leaf, score: 77.738 N N N N
vg0312772189 C -> T LOC_Os03g22270.2 upstream_gene_variant ; 3309.0bp to feature; MODIFIER silent_mutation Average:57.882; most accessible tissue: Zhenshan97 flag leaf, score: 77.738 N N N N
vg0312772189 C -> T LOC_Os03g22270.3 upstream_gene_variant ; 3309.0bp to feature; MODIFIER silent_mutation Average:57.882; most accessible tissue: Zhenshan97 flag leaf, score: 77.738 N N N N
vg0312772189 C -> T LOC_Os03g22270-LOC_Os03g22290 intergenic_region ; MODIFIER silent_mutation Average:57.882; most accessible tissue: Zhenshan97 flag leaf, score: 77.738 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0312772189 1.29E-06 8.60E-09 mr1422_2 Jap_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
vg0312772189 NA 9.21E-07 mr1583_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
vg0312772189 5.44E-06 4.82E-08 mr1653_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
vg0312772189 7.63E-10 6.60E-13 mr1850_2 Jap_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