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Detailed information for vg0900534728:

Variant ID: vg0900534728 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 534728
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 130. )

Flanking Sequence (100 bp) in Reference Genome:

AGGCTATTTCATTCTTGCAGTCAGCACATGGACAAACTATCTTCCTCATATTGTTCTTCTCAGCGTGTGCCTTGGCAATACCAATAAATTTAGACACTTC[G/A]
TTTCTATATGGAGACAAAAACCTCGGCCAATGATACATCCATTCCCGACTTTCCATATCTCTAAAAAAATACACATAAAATATTTGCACAATTAATACCA

Reverse complement sequence

TGGTATTAATTGTGCAAATATTTTATGTGTATTTTTTTAGAGATATGGAAAGTCGGGAATGGATGTATCATTGGCCGAGGTTTTTGTCTCCATATAGAAA[C/T]
GAAGTGTCTAAATTTATTGGTATTGCCAAGGCACACGCTGAGAAGAACAATATGAGGAAGATAGTTTGTCCATGTGCTGACTGCAAGAATGAAATAGCCT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.70%	6.10%	0.83%	4.42%	NA
All Indica	2759	98.30%	1.70%	0.00%	0.04%	NA
All Japonica	1512	68.60%	15.20%	2.51%	13.69%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	95.50%	4.40%	0.00%	0.17%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.00%	2.00%	0.00%	0.00%	NA
Temperate Japonica	767	52.80%	16.90%	4.69%	25.55%	NA
Tropical Japonica	504	93.50%	6.50%	0.00%	0.00%	NA
Japonica Intermediate	241	66.80%	27.80%	0.83%	4.56%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	90.00%	7.80%	1.11%	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
vg0900534728	G -> DEL	LOC_Os09g01770.1	N	frameshift_variant	Average:21.574; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0900534728	G -> A	LOC_Os09g01770.1	synonymous_variant ; p.Asn121Asn; LOW	synonymous_codon	Average:21.574; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0900534728	9.44E-07	NA	mr1008_2	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