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Detailed information for vg0329919537:

Variant ID: vg0329919537 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 29919537
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.60, A: 0.42, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

ATTGGAGCCGATAGCATGTACCTGACTACGTCGGCTTTGCATATAACAGTGCACTCGTTAGATAATAGATAATGCCTCAACCTTGTACACGAAAAATACA[A/G]
ACACAAGCATAACTTTTCCACAGGAGAATACCGAGTCTCAGCATCCAAGAGCCGTCGACTGAGATAAAATACAACTCGTTCCTTCCCTTCCAACTCTTGA

Reverse complement sequence

TCAAGAGTTGGAAGGGAAGGAACGAGTTGTATTTTATCTCAGTCGACGGCTCTTGGATGCTGAGACTCGGTATTCTCCTGTGGAAAAGTTATGCTTGTGT[T/C]
TGTATTTTTCGTGTACAAGGTTGAGGCATTATCTATTATCTAACGAGTGCACTGTTATATGCAAAGCCGACGTAGTCAGGTACATGCTATCGGCTCCAAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	39.10%	15.00%	8.97%	36.92%	NA
All Indica	2759	5.90%	24.90%	9.89%	59.26%	NA
All Japonica	1512	98.80%	0.70%	0.07%	0.46%	NA
Aus	269	20.40%	0.40%	51.30%	27.88%	NA
Indica I	595	5.70%	30.60%	8.24%	55.46%	NA
Indica II	465	5.80%	33.50%	8.17%	52.47%	NA
Indica III	913	4.30%	19.30%	11.61%	64.84%	NA
Indica Intermediate	786	8.10%	22.00%	10.18%	59.67%	NA
Temperate Japonica	767	99.50%	0.30%	0.00%	0.26%	NA
Tropical Japonica	504	97.80%	1.40%	0.20%	0.60%	NA
Japonica Intermediate	241	98.80%	0.40%	0.00%	0.83%	NA
VI/Aromatic	96	89.60%	1.00%	4.17%	5.21%	NA
Intermediate	90	53.30%	12.20%	8.89%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0329919537	A -> DEL	N	N	silent_mutation	Average:10.696; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0329919537	A -> G	LOC_Os03g52100.1	downstream_gene_variant ; 2220.0bp to feature; MODIFIER	silent_mutation	Average:10.696; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0329919537	A -> G	LOC_Os03g52110.1	intron_variant ; MODIFIER	silent_mutation	Average:10.696; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0329919537	6.99E-06	7.47E-06	mr1355_2	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