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Detailed information for vg0826915985:

Variant ID: vg0826915985 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 26915985
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTAACTATCGAGGTCGACCGAATTACACACCCAAACTCGAAAACCGGACATTCTACACCCTCAAGTATTGATACCGGGCAAATTACCCCCCTGAGCACTG[T/A]
TTTAGGTGGTTTTGGGATAGACTTGCTGACATGGCATTCCAGCGTGGCAAAAAAAAAATAATAATGGACCCACGTGTCAGTCTCTTTATCTCCTCTCTAT

Reverse complement sequence

ATAGAGAGGAGATAAAGAGACTGACACGTGGGTCCATTATTATTTTTTTTTTGCCACGCTGGAATGCCATGTCAGCAAGTCTATCCCAAAACCACCTAAA[A/T]
CAGTGCTCAGGGGGGTAATTTGCCCGGTATCAATACTTGAGGGTGTAGAATGTCCGGTTTTCGAGTTTGGGTGTGTAATTCGGTCGACCTCGATAGTTAG

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	84.20%	10.20%	0.11%	5.48%	NA
All Indica	2759	90.90%	0.10%	0.07%	8.99%	NA
All Japonica	1512	68.40%	31.10%	0.20%	0.33%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	89.70%	0.00%	0.00%	10.25%	NA
Indica II	465	96.30%	0.00%	0.00%	3.66%	NA
Indica III	913	86.90%	0.00%	0.11%	13.03%	NA
Indica Intermediate	786	93.10%	0.30%	0.13%	6.49%	NA
Temperate Japonica	767	91.00%	8.70%	0.13%	0.13%	NA
Tropical Japonica	504	41.50%	57.70%	0.20%	0.60%	NA
Japonica Intermediate	241	52.70%	46.50%	0.41%	0.41%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	86.70%	12.20%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0826915985	T -> A	LOC_Os08g42590.1	upstream_gene_variant ; 2209.0bp to feature; MODIFIER	silent_mutation	Average:59.985; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg0826915985	T -> A	LOC_Os08g42590.3	upstream_gene_variant ; 3018.0bp to feature; MODIFIER	silent_mutation	Average:59.985; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg0826915985	T -> A	LOC_Os08g42580.1	downstream_gene_variant ; 2356.0bp to feature; MODIFIER	silent_mutation	Average:59.985; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg0826915985	T -> A	LOC_Os08g42580.4	downstream_gene_variant ; 2356.0bp to feature; MODIFIER	silent_mutation	Average:59.985; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg0826915985	T -> A	LOC_Os08g42580-LOC_Os08g42590	intergenic_region ; MODIFIER	silent_mutation	Average:59.985; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg0826915985	T -> DEL	N	N	silent_mutation	Average:59.985; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0826915985	NA	7.39E-08	mr1554	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
vg0826915985	NA	8.73E-06	mr1263_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
vg0826915985	NA	1.85E-07	mr1668_2	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