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Detailed information for vg1200761506:

Variant ID: vg1200761506 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 761506
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGTCCCCCCCCTCTCTCTCTATATATATACACACATATATCTCTTTATTTTTTAGTGCTATCTAAATACTCCTCCGTTTCAGGTTATATGACGTTTTAA[C/T]
TTTGGTTAAAGTCAAACTACTCTAAGTTGAACTAATTCTATAGAAAAGTAATAATATTTACAATACCAGCATAGTTTCATTAAATCTATAATTGAATAAT

Reverse complement sequence

ATTATTCAATTATAGATTTAATGAAACTATGCTGGTATTGTAAATATTATTACTTTTCTATAGAATTAGTTCAACTTAGAGTAGTTTGACTTTAACCAAA[G/A]
TTAAAACGTCATATAACCTGAAACGGAGGAGTATTTAGATAGCACTAAAAAATAAAGAGATATATGTGTGTATATATATAGAGAGAGAGGGGGGGGACGT

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 92.90% 7.00% 0.06% 0.00% NA
All Indica  2759 87.90% 12.00% 0.11% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 72.90% 26.70% 0.33% 0.00% NA
Indica Intermediate  786 90.30% 9.70% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 0.00% 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
vg1200761506 C -> T LOC_Os12g02350.1 upstream_gene_variant ; 2285.0bp to feature; MODIFIER silent_mutation Average:58.451; most accessible tissue: Zhenshan97 flower, score: 93.405 N N N N
vg1200761506 C -> T LOC_Os12g02370.2 downstream_gene_variant ; 4928.0bp to feature; MODIFIER silent_mutation Average:58.451; most accessible tissue: Zhenshan97 flower, score: 93.405 N N N N
vg1200761506 C -> T LOC_Os12g02370.4 downstream_gene_variant ; 4928.0bp to feature; MODIFIER silent_mutation Average:58.451; most accessible tissue: Zhenshan97 flower, score: 93.405 N N N N
vg1200761506 C -> T LOC_Os12g02340.1 intron_variant ; MODIFIER silent_mutation Average:58.451; most accessible tissue: Zhenshan97 flower, score: 93.405 N N N N
vg1200761506 C -> T LOC_Os12g02340.2 intron_variant ; MODIFIER silent_mutation Average:58.451; most accessible tissue: Zhenshan97 flower, score: 93.405 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1200761506 NA 1.87E-06 mr1094 Ind_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
vg1200761506 NA 4.64E-07 mr1096 Ind_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
vg1200761506 NA 7.66E-06 mr1107 Ind_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
vg1200761506 NA 5.27E-08 mr1111 Ind_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
vg1200761506 NA 2.86E-08 mr1244 Ind_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