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Detailed information for vg0906168357:

Variant ID: vg0906168357 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6168357
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTACCTAGATATCTTAATATTGTGTGAAAACTGATTTTATCAGCATGTGTTTTATGCAGTGGGTTAAGTGCCATTTTGTTAAATGGGTGGATCCTGAAT[G/A]
GGATGAGCTGGCCGCAAAAACAATTTTATATCTTAGTGAGAGAAACATTGTGCTTCAGAAGTCGCTCGATGATGTGAACAAAAGTTGGATGTCTTTGTAC

Reverse complement sequence

GTACAAAGACATCCAACTTTTGTTCACATCATCGAGCGACTTCTGAAGCACAATGTTTCTCTCACTAAGATATAAAATTGTTTTTGCGGCCAGCTCATCC[C/T]
ATTCAGGATCCACCCATTTAACAAAATGGCACTTAACCCACTGCATAAAACACATGCTGATAAAATCAGTTTTCACACAATATTAAGATATCTAGGTAGA

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	76.70%	0.10%	4.89%	18.32%	NA
All Indica	2759	62.70%	0.10%	6.16%	31.06%	NA
All Japonica	1512	99.90%	0.00%	0.00%	0.13%	NA
Aus	269	78.10%	0.00%	21.19%	0.74%	NA
Indica I	595	47.90%	0.00%	2.86%	49.24%	NA
Indica II	465	79.60%	0.00%	1.94%	18.49%	NA
Indica III	913	57.70%	0.10%	11.28%	30.89%	NA
Indica Intermediate	786	69.60%	0.30%	5.22%	24.94%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	92.20%	0.00%	2.22%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906168357	G -> DEL	LOC_Os09g11130.1	N	frameshift_variant	Average:19.617; most accessible tissue: Zhenshan97 young leaf, score: 35.2	N	N	N	N
vg0906168357	G -> A	LOC_Os09g11130.1	stop_gained ; p.Trp57*; HIGH	stop_gained	Average:19.617; most accessible tissue: Zhenshan97 young leaf, score: 35.2	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906168357	NA	1.51E-06	mr1652	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