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Detailed information for vg0910968947:

Variant ID: vg0910968947 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10968947
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCAGTAAAAATGTCATTACTCCTTATTGGAAAGTCCAAATGACATGGGGTCAGTTTGGAAAGCTAACTTAATAAGCTTTCACACCATGTGCATAATGCAC[T/C]
ACGAAATATTGTAAATTGATACAGTTTTGCATGGAAAGTTGAATGTCTTGGCAGACTGTTGGCCTTCGGAGCAGTGTCCACTAATCTGGGCATAACTCTT

Reverse complement sequence

AAGAGTTATGCCCAGATTAGTGGACACTGCTCCGAAGGCCAACAGTCTGCCAAGACATTCAACTTTCCATGCAAAACTGTATCAATTTACAATATTTCGT[A/G]
GTGCATTATGCACATGGTGTGAAAGCTTATTAAGTTAGCTTTCCAAACTGACCCCATGTCATTTGGACTTTCCAATAAGGAGTAATGACATTTTTACTGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.20%	0.10%	0.42%	1.27%	NA
All Indica	2759	99.60%	0.20%	0.11%	0.14%	NA
All Japonica	1512	96.20%	0.00%	0.60%	3.17%	NA
Aus	269	95.90%	0.40%	2.97%	0.74%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.00%	0.22%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	99.00%	0.30%	0.38%	0.38%	NA
Temperate Japonica	767	97.00%	0.00%	0.00%	3.00%	NA
Tropical Japonica	504	96.00%	0.00%	1.79%	2.18%	NA
Japonica Intermediate	241	94.20%	0.00%	0.00%	5.81%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	95.60%	0.00%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910968947	T -> DEL	N	N	silent_mutation	Average:19.29; most accessible tissue: Callus, score: 34.325	N	N	N	N
vg0910968947	T -> C	LOC_Os09g17910.1	downstream_gene_variant ; 3446.0bp to feature; MODIFIER	silent_mutation	Average:19.29; most accessible tissue: Callus, score: 34.325	N	N	N	N
vg0910968947	T -> C	LOC_Os09g17920.1	downstream_gene_variant ; 1723.0bp to feature; MODIFIER	silent_mutation	Average:19.29; most accessible tissue: Callus, score: 34.325	N	N	N	N
vg0910968947	T -> C	LOC_Os09g17910-LOC_Os09g17920	intergenic_region ; MODIFIER	silent_mutation	Average:19.29; most accessible tissue: Callus, score: 34.325	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910968947	4.80E-06	6.98E-07	mr1449_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