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Detailed information for vg0906730370:

Variant ID: vg0906730370 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 6730370
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


AAGAATCTTGAGGTTGGAAGAGAAAATCCGCCATAGAAGAAGTGAGAAAATACCACGACCTCGTGTGTATCAGGGGTCGGGAAAGCTTCGCCGAACGCTG[G/A]
TCGCCACCCAATGATTTCCTTCGCCAGAAGAACGCCGTGCGCCACCATTTCTTTCAGATTCTCCTCCGTCACATTGGAGGGCGCCCACTGACTCTCGAAG

Reverse complement sequence

CTTCGAGAGTCAGTGGGCGCCCTCCAATGTGACGGAGGAGAATCTGAAAGAAATGGTGGCGCACGGCGTTCTTCTGGCGAAGGAAATCATTGGGTGGCGA[C/T]
CAGCGTTCGGCGAAGCTTTCCCGACCCCTGATACACACGAGGTCGTGGTATTTTCTCACTTCTTCTATGGCGGATTTTCTCTTCCAACCTCAAGATTCTT

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 88.60% 8.60% 1.27% 1.61% NA
All Indica  2759 98.40% 0.90% 0.36% 0.33% NA
All Japonica  1512 68.30% 24.40% 3.24% 4.10% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 93.80% 3.20% 1.94% 1.08% NA
Indica III  913 99.60% 0.30% 0.11% 0.00% NA
Indica Intermediate  786 98.70% 0.80% 0.00% 0.51% NA
Temperate Japonica  767 88.00% 11.50% 0.26% 0.26% NA
Tropical Japonica  504 31.00% 49.00% 8.93% 11.11% NA
Japonica Intermediate  241 83.40% 14.10% 0.83% 1.66% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 84.40% 8.90% 1.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0906730370 G -> DEL LOC_Os09g11950.1 N frameshift_variant Average:49.13; most accessible tissue: Minghui63 flag leaf, score: 72.907 N N N N
vg0906730370 G -> A LOC_Os09g11950.1 missense_variant ; p.Pro41Ser; MODERATE nonsynonymous_codon ; P41S Average:49.13; most accessible tissue: Minghui63 flag leaf, score: 72.907 possibly damaging 1.91 DELETERIOUS 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0906730370 3.99E-06 NA mr1227 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