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Detailed information for vg0625171406:

Variant ID: vg0625171406 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 25171406
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTCTCAAAAAGTTTAGCTAAGTTGACTTTAACCCCTAAACGAGTGATCTGCAAGTTTAGGAACCGGAATGACACAGTCGAACAAGTTTGAGGACCTGAA[C/T]
GGTCGATTTGCGAGTTTAGGGATCGGGATGACACAGCGGTACAAATTTATAGACCGGTGATGGACTTTACTCTTTTTTTTTCACCATGTTTGCAAGATAC

Reverse complement sequence

GTATCTTGCAAACATGGTGAAAAAAAAAGAGTAAAGTCCATCACCGGTCTATAAATTTGTACCGCTGTGTCATCCCGATCCCTAAACTCGCAAATCGACC[G/A]
TTCAGGTCCTCAAACTTGTTCGACTGTGTCATTCCGGTTCCTAAACTTGCAGATCACTCGTTTAGGGGTTAAAGTCAACTTAGCTAAACTTTTTGAGAGA

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 98.90% 0.60% 0.47% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 96.70% 1.90% 1.46% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 94.50% 2.90% 2.61% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 97.10% 2.50% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0625171406 C -> T LOC_Os06g41940.1 upstream_gene_variant ; 635.0bp to feature; MODIFIER silent_mutation Average:61.416; most accessible tissue: Minghui63 root, score: 91.589 N N N N
vg0625171406 C -> T LOC_Os06g41950.1 downstream_gene_variant ; 2089.0bp to feature; MODIFIER silent_mutation Average:61.416; most accessible tissue: Minghui63 root, score: 91.589 N N N N
vg0625171406 C -> T LOC_Os06g41930-LOC_Os06g41940 intergenic_region ; MODIFIER silent_mutation Average:61.416; most accessible tissue: Minghui63 root, score: 91.589 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0625171406 NA 5.88E-06 mr1071 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
vg0625171406 2.77E-06 NA mr1089 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
vg0625171406 6.00E-06 6.00E-06 mr1542 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
vg0625171406 NA 1.42E-06 mr1613 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
vg0625171406 NA 5.41E-06 mr1619 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
vg0625171406 NA 4.32E-06 mr1913 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