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Detailed information for vg0120180517:

Variant ID: vg0120180517 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 20180517
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGTGGCCGAGGTGCTACTATCAAAACCATGCACCCCAAGCCCAGCCTAAAACCATTTTGAGAGTTTTGAATAGAGGGAAAGGTGTGCATCCAATTCCAC[A/C]
ATAGTCCAACCATTCCATAAAGTCCAAGAGATATGAATATTCCCAAAGTCTAAAATTATAAAACCACCTAATGTTGTCTTTTTAATCAGCGAAGCATCTA

Reverse complement sequence

TAGATGCTTCGCTGATTAAAAAGACAACATTAGGTGGTTTTATAATTTTAGACTTTGGGAATATTCATATCTCTTGGACTTTATGGAATGGTTGGACTAT[T/G]
GTGGAATTGGATGCACACCTTTCCCTCTATTCAAAACTCTCAAAATGGTTTTAGGCTGGGCTTGGGGTGCATGGTTTTGATAGTAGCACCTCGGCCACAT

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	83.90%	7.50%	3.17%	5.46%	NA
All Indica	2759	89.40%	0.50%	3.26%	6.81%	NA
All Japonica	1512	70.20%	21.70%	3.51%	4.56%	NA
Aus	269	99.30%	0.00%	0.74%	0.00%	NA
Indica I	595	68.60%	0.20%	9.08%	22.18%	NA
Indica II	465	93.30%	1.10%	2.80%	2.80%	NA
Indica III	913	99.00%	0.10%	0.44%	0.44%	NA
Indica Intermediate	786	91.70%	0.90%	2.42%	4.96%	NA
Temperate Japonica	767	93.00%	5.50%	1.43%	0.13%	NA
Tropical Japonica	504	36.90%	43.70%	7.54%	11.90%	NA
Japonica Intermediate	241	67.60%	27.40%	1.66%	3.32%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	82.20%	11.10%	5.56%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0120180517	A -> DEL	N	N	silent_mutation	Average:32.951; most accessible tissue: Minghui63 flag leaf, score: 78.782	N	N	N	N
vg0120180517	A -> C	LOC_Os01g36370.1	downstream_gene_variant ; 3403.0bp to feature; MODIFIER	silent_mutation	Average:32.951; most accessible tissue: Minghui63 flag leaf, score: 78.782	N	N	N	N
vg0120180517	A -> C	LOC_Os01g36370-LOC_Os01g36380	intergenic_region ; MODIFIER	silent_mutation	Average:32.951; most accessible tissue: Minghui63 flag leaf, score: 78.782	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0120180517	NA	7.76E-06	mr1236	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
vg0120180517	NA	3.10E-07	mr1236	Jap_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
vg0120180517	NA	2.00E-10	mr1248	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
vg0120180517	NA	7.54E-12	mr1248	Jap_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
vg0120180517	NA	5.90E-10	mr1769	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
vg0120180517	NA	6.45E-13	mr1769	Jap_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
vg0120180517	NA	8.63E-06	mr1780	Jap_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
vg0120180517	NA	4.15E-07	mr1951	Jap_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
vg0120180517	NA	4.77E-14	mr1533_2	Jap_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
vg0120180517	NA	2.06E-07	mr1696_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