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Detailed information for vg0906841924:

Variant ID: vg0906841924 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6841924
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, T: 0.02, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

GTAATCCATGCATCGGACTTACCGATGTTTCTGGCACGAACTAGAGCCAAGTGCTCCTCAATGTAAGGAGCCACCAATGAAGATTGTTGCAGAACCGTGA[A/T]
ATGGGCTTTACGAAATAAATTGTTGTCTACCGTCATTATTGCTTTCCTTCCGAGAGTCCCTTTTCCCCGTAGTCTCTCTTCATGGCGTGATTCGGGTACC

Reverse complement sequence

GGTACCCGAATCACGCCATGAAGAGAGACTACGGGGAAAAGGGACTCTCGGAAGGAAAGCAATAATGACGGTAGACAACAATTTATTTCGTAAAGCCCAT[T/A]
TCACGGTTCTGCAACAATCTTCATTGGTGGCTCCTTACATTGAGGAGCACTTGGCTCTAGTTCGTGCCAGAAACATCGGTAAGTCCGATGCATGGATTAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	47.00%	40.10%	2.90%	9.97%	NA
All Indica	2759	72.50%	8.20%	2.94%	16.38%	NA
All Japonica	1512	11.70%	85.50%	2.45%	0.33%	NA
Aus	269	3.30%	87.70%	4.83%	4.09%	NA
Indica I	595	87.70%	1.50%	1.34%	9.41%	NA
Indica II	465	81.70%	15.10%	0.43%	2.80%	NA
Indica III	913	57.60%	6.10%	5.59%	30.67%	NA
Indica Intermediate	786	72.90%	11.50%	2.54%	13.10%	NA
Temperate Japonica	767	3.50%	95.30%	1.17%	0.00%	NA
Tropical Japonica	504	13.90%	84.90%	0.20%	0.99%	NA
Japonica Intermediate	241	33.20%	55.60%	11.20%	0.00%	NA
VI/Aromatic	96	3.10%	91.70%	4.17%	1.04%	NA
Intermediate	90	35.60%	60.00%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906841924	A -> DEL	N	N	silent_mutation	Average:34.464; most accessible tissue: Minghui63 young leaf, score: 60.103	N	N	N	N
vg0906841924	A -> T	LOC_Os09g12100.1	upstream_gene_variant ; 3856.0bp to feature; MODIFIER	silent_mutation	Average:34.464; most accessible tissue: Minghui63 young leaf, score: 60.103	N	N	N	N
vg0906841924	A -> T	LOC_Os09g12110.1	intron_variant ; MODIFIER	silent_mutation	Average:34.464; most accessible tissue: Minghui63 young leaf, score: 60.103	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906841924	3.99E-06	NA	mr1125_2	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