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Detailed information for vg0909300848:

Variant ID: vg0909300848 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9300848
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTAGGAAACCCTCTCGTACAAGAAATAAACTTTACATAACCACTCATATCAAATTTGGACTCCTTCCAAATTCGACTCCGCATCCCATACGCACACAA[T/A]
ACCTCCATCGTATACCATATGGAATCTTCACCAACCACGTGCATCAACTCTAGCCTAAGTATCCTGCATGATCTCTGACCATCACGGACGTCGCCTTATC

Reverse complement sequence

GATAAGGCGACGTCCGTGATGGTCAGAGATCATGCAGGATACTTAGGCTAGAGTTGATGCACGTGGTTGGTGAAGATTCCATATGGTATACGATGGAGGT[A/T]
TTGTGTGCGTATGGGATGCGGAGTCGAATTTGGAAGGAGTCCAAATTTGATATGAGTGGTTATGTAAAGTTTATTTCTTGTACGAGAGGGTTTCCTAAGG

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	81.70%	18.20%	0.06%	0.00%	NA
All Indica	2759	82.20%	17.70%	0.11%	0.00%	NA
All Japonica	1512	82.30%	17.70%	0.00%	0.00%	NA
Aus	269	69.10%	30.90%	0.00%	0.00%	NA
Indica I	595	82.20%	17.80%	0.00%	0.00%	NA
Indica II	465	88.40%	11.60%	0.00%	0.00%	NA
Indica III	913	77.80%	22.00%	0.22%	0.00%	NA
Indica Intermediate	786	83.80%	16.00%	0.13%	0.00%	NA
Temperate Japonica	767	88.70%	11.30%	0.00%	0.00%	NA
Tropical Japonica	504	81.90%	18.10%	0.00%	0.00%	NA
Japonica Intermediate	241	62.70%	37.30%	0.00%	0.00%	NA
VI/Aromatic	96	82.30%	17.70%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	0.00%	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
vg0909300848	T -> A	LOC_Os09g15260-LOC_Os09g15270	intergenic_region ; MODIFIER	silent_mutation	Average:33.352; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909300848	8.37E-06	1.57E-07	mr1386_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