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Detailed information for vg0920856743:

Variant ID: vg0920856743 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 20856743
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.56, G: 0.44, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


ATCTGTGTGCCAAGATGAAATATGACTATCGAAAGTAGGTGGAGAAAGTACTACACCCTCTGTCCCATAATATAAGGGATTTTAAGTTTTTACTTATAAT[A/G]
TTTGACCACTTGTCTTATTCAAAAAATTTGTGCAAATATAAAAAACGAAAAGTTGTGCTTAAAGTATTTTGGATAATAAAGTAAGTCACAAAGAAAATAA

Reverse complement sequence

TTATTTTCTTTGTGACTTACTTTATTATCCAAAATACTTTAAGCACAACTTTTCGTTTTTTATATTTGCACAAATTTTTTGAATAAGACAAGTGGTCAAA[T/C]
ATTATAAGTAAAAACTTAAAATCCCTTATATTATGGGACAGAGGGTGTAGTACTTTCTCCACCTACTTTCGATAGTCATATTTCATCTTGGCACACAGAT

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 63.60% 36.20% 0.21% 0.00% NA
All Indica  2759 44.40% 55.30% 0.29% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.07% 0.00% NA
Aus  269 39.40% 60.60% 0.00% 0.00% NA
Indica I  595 11.80% 87.70% 0.50% 0.00% NA
Indica II  465 59.80% 39.80% 0.43% 0.00% NA
Indica III  913 57.60% 42.40% 0.00% 0.00% NA
Indica Intermediate  786 44.70% 55.00% 0.38% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 81.10% 17.80% 1.11% 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
vg0920856743 A -> G LOC_Os09g36180.1 intron_variant ; MODIFIER silent_mutation Average:48.227; most accessible tissue: Zhenshan97 panicle, score: 72.468 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0920856743 NA 5.83E-06 mr1398 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
vg0920856743 NA 5.11E-10 mr1050_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
vg0920856743 NA 2.23E-13 mr1904_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