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Detailed information for vg0102459995:

Variant ID: vg0102459995 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 2459995
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, C: 0.06, others allele: 0.00, population size: 36. )

Flanking Sequence (100 bp) in Reference Genome:

ACATTGCCTGCCGATGCTTTTCGAGCCCGCAGATTATACTAGACTTGTTTGGTAGCACGCTATGTACTTCACAAGTGCGCATTCCGGTCATGAAAACTGC[A/C]
CTCAGGGAGACATATAATCATTTGTATCGCACATTAGGTCCCTTGATATTGTCTTTGATACCTTGTCAAAATGCTGAGAGTAAGTTTTTCTCTGTGCTGT

Reverse complement sequence

ACAGCACAGAGAAAAACTTACTCTCAGCATTTTGACAAGGTATCAAAGACAATATCAAGGGACCTAATGTGCGATACAAATGATTATATGTCTCCCTGAG[T/G]
GCAGTTTTCATGACCGGAATGCGCACTTGTGAAGTACATAGCGTGCTACCAAACAAGTCTAGTATAATCTGCGGGCTCGAAAAGCATCGGCAGGCAATGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	30.20%	18.00%	1.63%	50.13%	NA
All Indica	2759	12.10%	21.30%	0.76%	65.75%	NA
All Japonica	1512	56.50%	15.70%	3.31%	24.47%	NA
Aus	269	59.10%	5.90%	0.37%	34.57%	NA
Indica I	595	6.70%	61.80%	0.34%	31.09%	NA
Indica II	465	8.60%	3.90%	0.86%	86.67%	NA
Indica III	913	14.00%	8.90%	0.66%	76.45%	NA
Indica Intermediate	786	16.20%	15.50%	1.15%	67.18%	NA
Temperate Japonica	767	53.20%	3.90%	5.08%	37.81%	NA
Tropical Japonica	504	67.50%	25.20%	0.60%	6.75%	NA
Japonica Intermediate	241	44.40%	33.20%	3.32%	19.09%	NA
VI/Aromatic	96	38.50%	0.00%	3.12%	58.33%	NA
Intermediate	90	46.70%	11.10%	2.22%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0102459995	A -> DEL	N	N	silent_mutation	Average:41.675; most accessible tissue: Zhenshan97 flower, score: 85.482	N	N	N	N
vg0102459995	A -> C	LOC_Os01g05220-LOC_Os01g05240	intergenic_region ; MODIFIER	silent_mutation	Average:41.675; most accessible tissue: Zhenshan97 flower, score: 85.482	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0102459995	NA	4.80E-09	mr1352	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
vg0102459995	1.05E-06	NA	mr1669	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
vg0102459995	1.27E-06	2.62E-06	mr1669	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