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Detailed information for vg0911098439:

Variant ID: vg0911098439 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 11098439
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGCTGTAGCACTTGCTCCTCATCTCTCTAAATCTCTGAATATACTCATGCACAGGCTCATCATATCTCTGCTTGATCGCTGTTAAATCGGACAATTTCA[A/T]
CTCATGAATCTCACTGTAGAAATAGCTATGAAAATGCTTCTCCAAATCGGCCCAACTGTTGATTGATCCACATGGCAAAGAAGAAAGCCAAGTGAAAGCC

Reverse complement sequence

GGCTTTCACTTGGCTTTCTTCTTTGCCATGTGGATCAATCAACAGTTGGGCCGATTTGGAGAAGCATTTTCATAGCTATTTCTACAGTGAGATTCATGAG[T/A]
TGAAATTGTCCGATTTAACAGCGATCAAGCAGAGATATGATGAGCCTGTGCATGAGTATATTCAGAGATTTAGAGAGATGAGGAGCAAGTGCTACAGCTT

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	67.00%	2.10%	9.82%	21.07%	NA
All Indica	2759	62.80%	3.40%	14.53%	19.28%	NA
All Japonica	1512	86.20%	0.10%	1.12%	12.57%	NA
Aus	269	20.10%	0.70%	8.18%	71.00%	NA
Indica I	595	85.50%	1.00%	2.52%	10.92%	NA
Indica II	465	41.70%	2.40%	21.72%	34.19%	NA
Indica III	913	59.10%	6.10%	18.73%	15.99%	NA
Indica Intermediate	786	62.20%	2.70%	14.50%	20.61%	NA
Temperate Japonica	767	88.10%	0.00%	0.91%	10.95%	NA
Tropical Japonica	504	90.30%	0.20%	1.59%	7.94%	NA
Japonica Intermediate	241	71.80%	0.00%	0.83%	27.39%	NA
VI/Aromatic	96	18.80%	1.00%	13.54%	66.67%	NA
Intermediate	90	65.60%	1.10%	12.22%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0911098439	A -> DEL	N	N	silent_mutation	Average:42.622; most accessible tissue: Zhenshan97 young leaf, score: 64.747	N	N	N	N
vg0911098439	A -> T	LOC_Os09g18100.1	upstream_gene_variant ; 1527.0bp to feature; MODIFIER	silent_mutation	Average:42.622; most accessible tissue: Zhenshan97 young leaf, score: 64.747	N	N	N	N
vg0911098439	A -> T	LOC_Os09g18110.1	intron_variant ; MODIFIER	silent_mutation	Average:42.622; most accessible tissue: Zhenshan97 young leaf, score: 64.747	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0911098439	6.82E-07	6.82E-07	mr1374	Ind_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
vg0911098439	9.65E-07	9.65E-07	mr1964	Ind_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
vg0911098439	8.24E-06	8.24E-06	mr1972	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