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Detailed information for vg1101949649:

Variant ID: vg1101949649 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 1949649
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTAAGAATATGTTTTTAAATATTAAGTTGCAATTGGATACATGAAAATGACAATTCATAGGGATAAATTTGTTGTAAAAAATATTAACATGATATAATAA[C/A]
TTTTTGGGTTTATAAAACATAATCCTATTATATGTTTGTGATTTGTGCAGTATTAATCAAAGGTGACAAGTACGAGTACCTAATATAAACGAACAGTGTT

Reverse complement sequence

AACACTGTTCGTTTATATTAGGTACTCGTACTTGTCACCTTTGATTAATACTGCACAAATCACAAACATATAATAGGATTATGTTTTATAAACCCAAAAA[G/T]
TTATTATATCATGTTAATATTTTTTACAACAAATTTATCCCTATGAATTGTCATTTTCATGTATCCAATTGCAACTTAATATTTAAAAACATATTCTTAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.00% 2.30% 0.68% 0.00% NA
All Indica  2759 95.10% 3.80% 1.09% 0.00% NA
All Japonica  1512 99.70% 0.20% 0.07% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 79.60% 16.10% 4.30% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 95.40% 3.30% 1.27% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg1101949649 C -> A LOC_Os11g04600.1 upstream_gene_variant ; 1906.0bp to feature; MODIFIER silent_mutation Average:30.765; most accessible tissue: Minghui63 flower, score: 59.717 N N N N
vg1101949649 C -> A LOC_Os11g04590-LOC_Os11g04600 intergenic_region ; MODIFIER silent_mutation Average:30.765; most accessible tissue: Minghui63 flower, score: 59.717 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1101949649 NA 9.44E-06 mr1567_2 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
vg1101949649 NA 5.39E-06 mr1588_2 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
vg1101949649 NA 2.28E-09 mr1806_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