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Detailed information for vg0906199234:

Variant ID: vg0906199234 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6199234
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTGAATGGAAGAAGCTGCTTAATTTCTTCTCCTCTCCAGTGCTCCAGGTCAGGACTAAAATGGGTCCAGCCTTCGCCTTAGGCCATGTTTAGTTTTCAA[A/T]
CACAAATTTTTCGCCATATCAAATCGGATGTTTAGACACATGCAAGTATTAAATATGGAAAAAAACTAATTACATAAATTGAATGCAGATAGCGAGACAA

Reverse complement sequence

TTGTCTCGCTATCTGCATTCAATTTATGTAATTAGTTTTTTTCCATATTTAATACTTGCATGTGTCTAAACATCCGATTTGATATGGCGAAAAATTTGTG[T/A]
TTGAAAACTAAACATGGCCTAAGGCGAAGGCTGGACCCATTTTAGTCCTGACCTGGAGCACTGGAGAGGAGAAGAAATTAAGCAGCTTCTTCCATTCAGA

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	67.40%	4.40%	1.14%	27.04%	NA
All Indica	2759	65.30%	5.20%	1.49%	28.02%	NA
All Japonica	1512	75.70%	3.60%	0.20%	20.50%	NA
Aus	269	58.40%	0.40%	2.97%	38.29%	NA
Indica I	595	83.70%	12.30%	0.34%	3.70%	NA
Indica II	465	41.90%	0.40%	2.80%	54.84%	NA
Indica III	913	68.50%	3.50%	1.20%	26.83%	NA
Indica Intermediate	786	61.50%	4.70%	1.91%	31.93%	NA
Temperate Japonica	767	89.30%	0.10%	0.13%	10.43%	NA
Tropical Japonica	504	69.00%	9.10%	0.40%	21.43%	NA
Japonica Intermediate	241	46.50%	2.90%	0.00%	50.62%	NA
VI/Aromatic	96	19.80%	7.30%	0.00%	72.92%	NA
Intermediate	90	70.00%	3.30%	2.22%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906199234	A -> DEL	N	N	silent_mutation	Average:26.282; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg0906199234	A -> T	LOC_Os09g11170.1	downstream_gene_variant ; 2317.0bp to feature; MODIFIER	silent_mutation	Average:26.282; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg0906199234	A -> T	LOC_Os09g11180.1	downstream_gene_variant ; 1403.0bp to feature; MODIFIER	silent_mutation	Average:26.282; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg0906199234	A -> T	LOC_Os09g11180-LOC_Os09g11190	intergenic_region ; MODIFIER	silent_mutation	Average:26.282; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906199234	2.25E-06	3.39E-06	mr1160_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
vg0906199234	NA	9.44E-06	mr1768_2	Ind_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