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Detailed information for vg0709162379:

Variant ID: vg0709162379 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 9162379
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


CTGAAATTGACTTAGGAGTGTCGTCCATGAGGTACACAGTGAAATCATCACCAAAAGACTTAGTCGTCCTTTGTCTTTTACTCCTTCGAGGAGCTTCACT[G/A]
TCATCCTCCTCAGTGACATGTTCGTGTGTATGTTCAGTTTGTTCTGGTGGTGTGATTGAATTGGGAATTATTTCAGAGGTTTGACTAGAACTACTATGTG

Reverse complement sequence

CACATAGTAGTTCTAGTCAAACCTCTGAAATAATTCCCAATTCAATCACACCACCAGAACAAACTGAACATACACACGAACATGTCACTGAGGAGGATGA[C/T]
AGTGAAGCTCCTCGAAGGAGTAAAAGACAAAGGACGACTAAGTCTTTTGGTGATGATTTCACTGTGTACCTCATGGACGACACTCCTAAGTCAATTTCAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.60% 1.50% 0.74% 11.19% NA
All Indica  2759 78.30% 2.10% 0.58% 19.03% NA
All Japonica  1512 97.80% 0.90% 1.26% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 37.50% 0.20% 1.68% 60.67% NA
Indica II  465 93.50% 0.00% 0.00% 6.45% NA
Indica III  913 99.70% 0.00% 0.00% 0.33% NA
Indica Intermediate  786 75.40% 7.10% 0.76% 16.67% NA
Temperate Japonica  767 96.50% 1.80% 1.69% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 0.00% 2.49% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 0.00% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0709162379 G -> DEL N N silent_mutation Average:22.484; most accessible tissue: Minghui63 root, score: 40.262 N N N N
vg0709162379 G -> A LOC_Os07g15780.1 intron_variant ; MODIFIER silent_mutation Average:22.484; most accessible tissue: Minghui63 root, score: 40.262 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0709162379 7.86E-08 7.86E-08 mr1270 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