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Detailed information for vg0713863434:

Variant ID: vg0713863434 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 13863434
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.04, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

GGACATATGAGAGGTTTTCAGGTGAATTCGGCTAAGATTATCAACAAGTATCAGAGGAAATATGATAAGCAGCAGGAGAAGTATTATGAGGAAGAAGATG[A/G]
CGGCTTTGATCCTCATTGGGGTTGTGAGTTATTTAGATTTTGTTGGAACGAAGGTATGAGGCTGCCATCAATCGAAAAATGTCCTGGTTGCAATGATATT

Reverse complement sequence

AATATCATTGCAACCAGGACATTTTTCGATTGATGGCAGCCTCATACCTTCGTTCCAACAAAATCTAAATAACTCACAACCCCAATGAGGATCAAAGCCG[T/C]
CATCTTCTTCCTCATAATACTTCTCCTGCTGCTTATCATATTTCCTCTGATACTTGTTGATAATCTTAGCCGAATTCACCTGAAAACCTCTCATATGTCC

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	49.70%	32.70%	0.40%	17.22%	NA
All Indica	2759	31.20%	54.30%	0.51%	13.95%	NA
All Japonica	1512	71.20%	0.90%	0.20%	27.78%	NA
Aus	269	98.90%	0.70%	0.00%	0.37%	NA
Indica I	595	31.60%	40.30%	0.67%	27.39%	NA
Indica II	465	13.50%	80.40%	0.00%	6.02%	NA
Indica III	913	39.30%	54.80%	0.44%	5.48%	NA
Indica Intermediate	786	32.10%	48.90%	0.76%	18.32%	NA
Temperate Japonica	767	65.40%	1.00%	0.26%	33.25%	NA
Tropical Japonica	504	92.10%	0.40%	0.00%	7.54%	NA
Japonica Intermediate	241	45.60%	1.20%	0.41%	52.70%	NA
VI/Aromatic	96	94.80%	0.00%	0.00%	5.21%	NA
Intermediate	90	57.80%	36.70%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0713863434	A -> DEL	N	N	silent_mutation	Average:39.868; most accessible tissue: Zhenshan97 young leaf, score: 69.723	N	N	N	N
vg0713863434	A -> G	LOC_Os07g24350-LOC_Os07g24370	intergenic_region ; MODIFIER	silent_mutation	Average:39.868; most accessible tissue: Zhenshan97 young leaf, score: 69.723	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0713863434	NA	7.93E-08	mr1212	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
vg0713863434	3.90E-06	3.07E-06	mr1719	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
vg0713863434	NA	2.28E-08	mr1929	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
vg0713863434	NA	6.35E-06	mr1428_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