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Detailed information for vg0630268417:

Variant ID: vg0630268417 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 30268417
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTCTCCATTTCAACCACACAATGGTACATATTGTTGGCAACTTTTTTGGCAAGTAGACAAACATAATCGCAACACCTAAACGCTTTGCGGTGATTGTAG[A/T]
GTCACAAATCACCCTAATCACTACCATATTTCACATGACAACAAATGATCCATTATCATTACAATAAATTTACGTCACGAAACATGAGCATATCTATTCA

Reverse complement sequence

TGAATAGATATGCTCATGTTTCGTGACGTAAATTTATTGTAATGATAATGGATCATTTGTTGTCATGTGAAATATGGTAGTGATTAGGGTGATTTGTGAC[T/A]
CTACAATCACCGCAAAGCGTTTAGGTGTTGCGATTATGTTTGTCTACTTGCCAAAAAAGTTGCCAACAATATGTACCATTGTGTGGTTGAAATGGAGAAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 68.20% 31.80% 0.08% 0.00% NA
All Indica  2759 96.10% 3.90% 0.04% 0.00% NA
All Japonica  1512 24.90% 75.10% 0.00% 0.00% NA
Aus  269 46.50% 53.20% 0.37% 0.00% NA
Indica I  595 93.60% 6.40% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 92.70% 7.10% 0.13% 0.00% NA
Temperate Japonica  767 6.90% 93.10% 0.00% 0.00% NA
Tropical Japonica  504 57.90% 42.10% 0.00% 0.00% NA
Japonica Intermediate  241 12.90% 87.10% 0.00% 0.00% NA
VI/Aromatic  96 6.20% 92.70% 1.04% 0.00% NA
Intermediate  90 70.00% 28.90% 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
vg0630268417 A -> T LOC_Os06g49970.2 downstream_gene_variant ; 1502.0bp to feature; MODIFIER silent_mutation Average:46.589; most accessible tissue: Callus, score: 64.06 N N N N
vg0630268417 A -> T LOC_Os06g49980.1 downstream_gene_variant ; 1502.0bp to feature; MODIFIER silent_mutation Average:46.589; most accessible tissue: Callus, score: 64.06 N N N N
vg0630268417 A -> T LOC_Os06g49970-LOC_Os06g49980 intergenic_region ; MODIFIER silent_mutation Average:46.589; most accessible tissue: Callus, score: 64.06 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0630268417 NA 4.87E-19 mr1422 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
vg0630268417 NA 1.63E-06 mr1553_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
vg0630268417 NA 2.66E-08 mr1623_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
vg0630268417 NA 2.21E-08 mr1705_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
vg0630268417 NA 1.10E-07 mr1817_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