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Detailed information for vg0906910944:

Variant ID: vg0906910944 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6910944
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGCTAGGTAGCTAGCCAGGATGTGTAAAGAAATAGGGGCACGAGAAAATGGCTGTACAAAAGACATTGAAGACAACACATGGTAATTATTAATTCGTTCT[G/T]
CACCAAGTTCTAAACATATCAATTTCAAGAAGACACAAAAATTTCTCTAGCTGACAGCTGTCCATATATATGAAATTATCGATTACTCCAAAGTTTGTCA

Reverse complement sequence

TGACAAACTTTGGAGTAATCGATAATTTCATATATATGGACAGCTGTCAGCTAGAGAAATTTTTGTGTCTTCTTGAAATTGATATGTTTAGAACTTGGTG[C/A]
AGAACGAATTAATAATTACCATGTGTTGTCTTCAATGTCTTTTGTACAGCCATTTTCTCGTGCCCCTATTTCTTTACACATCCTGGCTAGCTACCTAGCG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.00%	7.90%	0.17%	0.00%	NA
All Indica	2759	99.20%	0.80%	0.04%	0.00%	NA
All Japonica	1512	84.60%	15.10%	0.33%	0.00%	NA
Aus	269	71.40%	28.60%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.60%	0.20%	0.22%	0.00%	NA
Indica III	913	98.70%	1.30%	0.00%	0.00%	NA
Indica Intermediate	786	99.00%	1.00%	0.00%	0.00%	NA
Temperate Japonica	767	81.20%	18.50%	0.26%	0.00%	NA
Tropical Japonica	504	90.90%	8.90%	0.20%	0.00%	NA
Japonica Intermediate	241	82.20%	17.00%	0.83%	0.00%	NA
VI/Aromatic	96	60.40%	39.60%	0.00%	0.00%	NA
Intermediate	90	90.00%	7.80%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906910944	G -> T	LOC_Os09g12200-LOC_Os09g12210	intergenic_region ; MODIFIER	silent_mutation	Average:36.85; most accessible tissue: Callus, score: 71.777	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906910944	NA	1.33E-06	mr1060_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
vg0906910944	NA	2.87E-06	mr1296_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
vg0906910944	3.81E-06	3.81E-06	mr1360_2	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