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Detailed information for vg0910456701:

Variant ID: vg0910456701 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10456701
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGTATGGTATATGTGCTGGTTTTTTAAAAGAACCGGCACCTCTAATATATTATGGGTGTTGGTTTTTAATTAACTGGTACATATAATATATTATAGGTT[C/T]
CAGTTCTTTTAGAAAAGGTGCCGGTTTTAGCTAATGAACTGGCACTTATGCTTCCTTAAAGGTGCCGGTTCTTTATTTTTTTTTGGCGTGCGAATGTGGG

Reverse complement sequence

CCCACATTCGCACGCCAAAAAAAAATAAAGAACCGGCACCTTTAAGGAAGCATAAGTGCCAGTTCATTAGCTAAAACCGGCACCTTTTCTAAAAGAACTG[G/A]
AACCTATAATATATTATATGTACCAGTTAATTAAAAACCAACACCCATAATATATTAGAGGTGCCGGTTCTTTTAAAAAACCAGCACATATACCATACCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.50%	1.80%	2.26%	54.42%	NA
All Indica	2759	9.40%	0.00%	1.16%	89.45%	NA
All Japonica	1512	87.20%	5.60%	4.83%	2.31%	NA
Aus	269	85.90%	0.00%	0.00%	14.13%	NA
Indica I	595	14.60%	0.00%	2.52%	82.86%	NA
Indica II	465	10.10%	0.00%	1.51%	88.39%	NA
Indica III	913	4.50%	0.00%	0.11%	95.40%	NA
Indica Intermediate	786	10.70%	0.00%	1.15%	88.17%	NA
Temperate Japonica	767	78.60%	11.00%	9.26%	1.17%	NA
Tropical Japonica	504	97.20%	0.00%	0.20%	2.58%	NA
Japonica Intermediate	241	93.80%	0.40%	0.41%	5.39%	NA
VI/Aromatic	96	93.80%	0.00%	0.00%	6.25%	NA
Intermediate	90	70.00%	0.00%	2.22%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910456701	C -> DEL	N	N	silent_mutation	Average:13.177; most accessible tissue: Callus, score: 73.943	N	N	N	N
vg0910456701	C -> T	LOC_Os09g17060.1	upstream_gene_variant ; 2072.0bp to feature; MODIFIER	silent_mutation	Average:13.177; most accessible tissue: Callus, score: 73.943	N	N	N	N
vg0910456701	C -> T	LOC_Os09g17049.1	downstream_gene_variant ; 3933.0bp to feature; MODIFIER	silent_mutation	Average:13.177; most accessible tissue: Callus, score: 73.943	N	N	N	N
vg0910456701	C -> T	LOC_Os09g17070.1	downstream_gene_variant ; 4548.0bp to feature; MODIFIER	silent_mutation	Average:13.177; most accessible tissue: Callus, score: 73.943	N	N	N	N
vg0910456701	C -> T	LOC_Os09g17049.2	downstream_gene_variant ; 3933.0bp to feature; MODIFIER	silent_mutation	Average:13.177; most accessible tissue: Callus, score: 73.943	N	N	N	N
vg0910456701	C -> T	LOC_Os09g17060-LOC_Os09g17070	intergenic_region ; MODIFIER	silent_mutation	Average:13.177; most accessible tissue: Callus, score: 73.943	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910456701	NA	4.67E-06	mr1354	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0910456701	1.62E-06	1.62E-06	mr1499_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