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Detailed information for vg0613263498:

Variant ID: vg0613263498 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 13263498
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


GGCTCGGTACTTGCAAGGGGTGCGCCGTTATCATAATCGCAATGTTCGATCACGAGCTTTTTTAGTCGGCGACCTGGTTCTGAGAAAAATTCAAACTACA[C/T]
AGGATCGGCACAAGTTATCTCCCTTATGGGAAGGACCATTCATAATTTCCAAAGTCACTCGGCCAGGTTCTTACCGACTCAAGCGTGAAGACGGTACTCC

Reverse complement sequence

GGAGTACCGTCTTCACGCTTGAGTCGGTAAGAACCTGGCCGAGTGACTTTGGAAATTATGAATGGTCCTTCCCATAAGGGAGATAACTTGTGCCGATCCT[G/A]
TGTAGTTTGAATTTTTCTCAGAACCAGGTCGCCGACTAAAAAAGCTCGTGATCGAACATTGCGATTATGATAACGGCGCACCCCTTGCAAGTACCGAGCC

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 50.00% 49.70% 0.21% 0.13% NA
All Indica  2759 21.20% 78.40% 0.25% 0.18% NA
All Japonica  1512 97.60% 2.30% 0.13% 0.00% NA
Aus  269 61.30% 38.30% 0.37% 0.00% NA
Indica I  595 19.30% 80.20% 0.34% 0.17% NA
Indica II  465 9.90% 89.70% 0.22% 0.22% NA
Indica III  913 28.50% 71.10% 0.22% 0.22% NA
Indica Intermediate  786 20.90% 78.80% 0.25% 0.13% NA
Temperate Japonica  767 96.50% 3.50% 0.00% 0.00% NA
Tropical Japonica  504 98.80% 1.00% 0.20% 0.00% NA
Japonica Intermediate  241 98.30% 1.20% 0.41% 0.00% NA
VI/Aromatic  96 85.40% 14.60% 0.00% 0.00% NA
Intermediate  90 60.00% 38.90% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0613263498 C -> T LOC_Os06g22770.1 downstream_gene_variant ; 1222.0bp to feature; MODIFIER silent_mutation Average:35.469; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 N N N N
vg0613263498 C -> T LOC_Os06g22790.1 downstream_gene_variant ; 476.0bp to feature; MODIFIER silent_mutation Average:35.469; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 N N N N
vg0613263498 C -> T LOC_Os06g22780.1 intron_variant ; MODIFIER silent_mutation Average:35.469; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 N N N N
vg0613263498 C -> DEL N N silent_mutation Average:35.469; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0613263498 3.86E-06 NA mr1141_2 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