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Detailed information for vg0719581422:

Variant ID: vg0719581422 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 19581422
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTGTGCTAAACGCTTTCCTATTTTCGTGCCCTAATTCACCTTCGCGTTCATCTTCCGTAGAAAACAAACATCACTGCGATACTATTTGAGAAGCTTCTG[A/C]
CAGCTGCAGTTTCTTCTAGAATCTTAAGATGTACGAAGCTCTCTCAAACAATTTATATTTTCATTTATATTTTGAGAATCTATAATTATAGAATTTAAAA

Reverse complement sequence

TTTTAAATTCTATAATTATAGATTCTCAAAATATAAATGAAAATATAAATTGTTTGAGAGAGCTTCGTACATCTTAAGATTCTAGAAGAAACTGCAGCTG[T/G]
CAGAAGCTTCTCAAATAGTATCGCAGTGATGTTTGTTTTCTACGGAAGATGAACGCGAAGGTGAATTAGGGCACGAAAATAGGAAAGCGTTTAGCACAAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.70% 9.30% 0.00% 0.00% NA
All Indica  2759 85.20% 14.80% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 90.70% 9.30% 0.00% 0.00% NA
Indica I  595 92.60% 7.40% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 72.80% 27.20% 0.00% 0.00% NA
Indica Intermediate  786 85.40% 14.60% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 0.00% 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
vg0719581422 A -> C LOC_Os07g32750-LOC_Os07g32761 intergenic_region ; MODIFIER silent_mutation Average:23.933; most accessible tissue: Zhenshan97 panicle, score: 36.038 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0719581422 4.46E-06 4.45E-06 mr1996 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
vg0719581422 NA 8.64E-06 mr1380_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
vg0719581422 NA 8.80E-07 mr1561_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
vg0719581422 NA 5.16E-06 mr1996_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