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Detailed information for vg0909870169:

Variant ID: vg0909870169 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9870169
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTCAAGTTTAGTCGAAATTTTTGTAAGGAGTGCTGTTGGTGCACTTTGTAAACACAGAGAGAATCAATAAAGTCGTCATCCACTTTAAGAATTCTTCG[A/T]
TTTGTGTTTCACCGGGTTTCGGTGGTCTAACCGGCGACCCACCGGCGGTTAGAACGACGGCATCGCGGCGGTCAGACCGGCAGGTGCAAGGCGGTCAGAC

Reverse complement sequence

GTCTGACCGCCTTGCACCTGCCGGTCTGACCGCCGCGATGCCGTCGTTCTAACCGCCGGTGGGTCGCCGGTTAGACCACCGAAACCCGGTGAAACACAAA[T/A]
CGAAGAATTCTTAAAGTGGATGACGACTTTATTGATTCTCTCTGTGTTTACAAAGTGCACCAACAGCACTCCTTACAAAAATTTCGACTAAACTTGAAAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	29.20%	0.20%	10.94%	59.69%	NA
All Indica	2759	16.80%	0.10%	13.70%	69.34%	NA
All Japonica	1512	53.60%	0.00%	0.60%	45.77%	NA
Aus	269	16.70%	1.90%	43.49%	37.92%	NA
Indica I	595	9.90%	0.00%	6.05%	84.03%	NA
Indica II	465	20.20%	0.00%	9.25%	70.54%	NA
Indica III	913	20.50%	0.20%	20.37%	58.93%	NA
Indica Intermediate	786	15.80%	0.30%	14.38%	69.59%	NA
Temperate Japonica	767	77.30%	0.00%	0.52%	22.16%	NA
Tropical Japonica	504	9.10%	0.00%	0.99%	89.88%	NA
Japonica Intermediate	241	71.40%	0.00%	0.00%	28.63%	NA
VI/Aromatic	96	33.30%	0.00%	4.17%	62.50%	NA
Intermediate	90	30.00%	0.00%	10.00%	60.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909870169	A -> DEL	N	N	silent_mutation	Average:9.689; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0909870169	A -> T	LOC_Os09g16180.1	downstream_gene_variant ; 4932.0bp to feature; MODIFIER	silent_mutation	Average:9.689; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0909870169	A -> T	LOC_Os09g16180-LOC_Os09g16190	intergenic_region ; MODIFIER	silent_mutation	Average:9.689; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909870169	3.06E-06	3.06E-06	mr1355	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