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Detailed information for vg0707567583:

Variant ID: vg0707567583 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 7567583
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.77, G: 0.23, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:


ACCTGAATAAAGCATGTCCGAAAGACGACTTCCCCTTGCCGCGAATCGACCAACTCTGGGGGCGAAGAGGGGCGCGAAGTATCGCTCGAACTCTTAGAAG[G/A]
AGTAAGGGTCGAAGCGCTCGAGCACATGCACAAGTACGCCACAAGCACTTCGGCAACTTACAACAAAAAAGTTCGACCCACGCAGCTGATGCCTGGTCAT

Reverse complement sequence

ATGACCAGGCATCAGCTGCGTGGGTCGAACTTTTTTGTTGTAAGTTGCCGAAGTGCTTGTGGCGTACTTGTGCATGTGCTCGAGCGCTTCGACCCTTACT[C/T]
CTTCTAAGAGTTCGAGCGATACTTCGCGCCCCTCTTCGCCCCCAGAGTTGGTCGATTCGCGGCAAGGGGAAGTCGTCTTTCGGACATGCTTTATTCAGGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.50% 34.90% 1.38% 4.25% NA
All Indica  2759 93.30% 6.20% 0.25% 0.25% NA
All Japonica  1512 5.30% 79.70% 2.45% 12.57% NA
Aus  269 33.50% 59.10% 7.43% 0.00% NA
Indica I  595 98.00% 2.00% 0.00% 0.00% NA
Indica II  465 91.20% 7.10% 0.65% 1.08% NA
Indica III  913 96.80% 2.60% 0.44% 0.11% NA
Indica Intermediate  786 87.00% 12.80% 0.00% 0.13% NA
Temperate Japonica  767 1.20% 95.80% 0.39% 2.61% NA
Tropical Japonica  504 12.10% 68.30% 6.15% 13.49% NA
Japonica Intermediate  241 4.10% 52.30% 1.24% 42.32% NA
VI/Aromatic  96 24.00% 76.00% 0.00% 0.00% NA
Intermediate  90 47.80% 46.70% 1.11% 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
vg0707567583 G -> DEL LOC_Os07g13190.1 N frameshift_variant Average:39.022; most accessible tissue: Minghui63 young leaf, score: 74.007 N N N N
vg0707567583 G -> A LOC_Os07g13190.1 synonymous_variant ; p.Arg896Arg; LOW synonymous_codon Average:39.022; most accessible tissue: Minghui63 young leaf, score: 74.007 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0707567583 NA 1.17E-12 mr1056 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
vg0707567583 NA 5.51E-10 mr1195 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
vg0707567583 NA 6.81E-12 mr1329 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
vg0707567583 NA 6.48E-13 mr1362 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
vg0707567583 NA 2.12E-10 mr1379 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
vg0707567583 NA 1.10E-07 mr1559 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
vg0707567583 NA 2.92E-10 mr1581 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
vg0707567583 NA 3.28E-07 mr1716 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
vg0707567583 NA 6.55E-08 mr1804 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
vg0707567583 NA 9.80E-14 mr1982 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
vg0707567583 NA 5.79E-09 mr1379_2 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
vg0707567583 NA 5.38E-17 mr1457_2 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
vg0707567583 2.30E-06 NA mr1543_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
vg0707567583 NA 2.19E-06 mr1559_2 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
vg0707567583 NA 7.53E-08 mr1690_2 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