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Detailed information for vg0717918985:

Variant ID: vg0717918985 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 17918985
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

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

Flanking Sequence (100 bp) in Reference Genome:

CCATGTCAAGTCGTTGTCTTATATCGTTGTGTTAGTTTGCTTGTTTTAAGTTTGGTTGTGTGTGTCTCGCATGTAATTTACATCAGTGGTGGGATGTAAG[A/T]
GCATGCGTTTGTTTGCTTTTGAGTGTTAGGAAGTTGGTGAGTTTAGTGGTGTGAGAGTCTTCAGTTTTGTAATAATGAAACTCAGTTAAGATCAATAAAA

Reverse complement sequence

TTTTATTGATCTTAACTGAGTTTCATTATTACAAAACTGAAGACTCTCACACCACTAAACTCACCAACTTCCTAACACTCAAAAGCAAACAAACGCATGC[T/A]
CTTACATCCCACCACTGATGTAAATTACATGCGAGACACACACAACCAAACTTAAAACAAGCAAACTAACACAACGATATAAGACAACGACTTGACATGG

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	73.00%	4.40%	18.49%	4.08%	NA
All Indica	2759	70.10%	7.00%	22.87%	0.04%	NA
All Japonica	1512	74.70%	0.20%	12.57%	12.50%	NA
Aus	269	84.00%	3.00%	12.27%	0.74%	NA
Indica I	595	90.40%	1.80%	7.73%	0.00%	NA
Indica II	465	51.60%	10.80%	37.63%	0.00%	NA
Indica III	913	66.70%	8.50%	24.75%	0.00%	NA
Indica Intermediate	786	69.70%	6.70%	23.41%	0.13%	NA
Temperate Japonica	767	72.60%	0.10%	6.91%	20.34%	NA
Tropical Japonica	504	73.20%	0.40%	22.02%	4.37%	NA
Japonica Intermediate	241	84.60%	0.00%	10.79%	4.56%	NA
VI/Aromatic	96	92.70%	2.10%	4.17%	1.04%	NA
Intermediate	90	80.00%	2.20%	17.78%	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
vg0717918985	A -> DEL	N	N	silent_mutation	Average:33.352; most accessible tissue: Zhenshan97 flag leaf, score: 58.104	N	N	N	N
vg0717918985	A -> T	LOC_Os07g30310.1	intron_variant ; MODIFIER	silent_mutation	Average:33.352; most accessible tissue: Zhenshan97 flag leaf, score: 58.104	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0717918985	3.65E-06	NA	mr1211_2	Jap_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