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Detailed information for vg0911695608:

Variant ID: vg0911695608 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 11695608
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGCGAGAGCTTGAGATTTCACCCTAAGCCCCCGGCCGAACTGGCAAAGGGGGGCCTGCGCGGTCTCCCGGTGAGGAGCCACGAGCTCCGTCAGTTTTAG[T/C]
TAACCAAATTATTCCTTTTATTCAACTTAAATAGGAAGTAGCATGTTCTGAACCTACAACTTGAGAGTCATGCACATATAAAACACTATATGCCTAAAAC

Reverse complement sequence

GTTTTAGGCATATAGTGTTTTATATGTGCATGACTCTCAAGTTGTAGGTTCAGAACATGCTACTTCCTATTTAAGTTGAATAAAAGGAATAATTTGGTTA[A/G]
CTAAAACTGACGGAGCTCGTGGCTCCTCACCGGGAGACCGCGCAGGCCCCCCTTTGCCAGTTCGGCCGGGGGCTTAGGGTGAAATCTCAAGCTCTCGCTC

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	89.20%	1.30%	4.40%	5.08%	NA
All Indica	2759	86.40%	1.40%	3.91%	8.30%	NA
All Japonica	1512	98.30%	0.00%	1.46%	0.26%	NA
Aus	269	69.10%	5.20%	24.16%	1.49%	NA
Indica I	595	92.10%	0.30%	2.52%	5.04%	NA
Indica II	465	95.30%	0.90%	1.08%	2.80%	NA
Indica III	913	77.00%	1.50%	5.70%	15.77%	NA
Indica Intermediate	786	87.80%	2.30%	4.58%	5.34%	NA
Temperate Japonica	767	99.60%	0.00%	0.26%	0.13%	NA
Tropical Japonica	504	96.00%	0.00%	3.77%	0.20%	NA
Japonica Intermediate	241	98.80%	0.00%	0.41%	0.83%	NA
VI/Aromatic	96	84.40%	7.30%	8.33%	0.00%	NA
Intermediate	90	88.90%	2.20%	5.56%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0911695608	T -> DEL	N	N	silent_mutation	Average:15.931; most accessible tissue: Zhenshan97 flag leaf, score: 39.979	N	N	N	N
vg0911695608	T -> C	LOC_Os09g19540.1	upstream_gene_variant ; 1683.0bp to feature; MODIFIER	silent_mutation	Average:15.931; most accessible tissue: Zhenshan97 flag leaf, score: 39.979	N	N	N	N
vg0911695608	T -> C	LOC_Os09g19550.1	upstream_gene_variant ; 4864.0bp to feature; MODIFIER	silent_mutation	Average:15.931; most accessible tissue: Zhenshan97 flag leaf, score: 39.979	N	N	N	N
vg0911695608	T -> C	LOC_Os09g19540-LOC_Os09g19550	intergenic_region ; MODIFIER	silent_mutation	Average:15.931; most accessible tissue: Zhenshan97 flag leaf, score: 39.979	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0911695608	1.39E-06	7.02E-06	mr1304	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