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Detailed information for vg0826363216:

Variant ID: vg0826363216 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 26363216
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTCCGTGCGCCGACATGCCACCACGACATACCGGAAAGAGGCCGTGACAGGACCCTTCGCATAACCCCCCTCTAACCGATCGCACCACACCTTAGGGTT[C/T]
GCCCCCGTCCCCAGCAGGCAACGGGCAGCCCCCCTTTCGTGCCGCAGTGAATCCAGAAGCCGATCAACCGGACACCTCGGCCGACCCAACTCCATCACGC

Reverse complement sequence

GCGTGATGGAGTTGGGTCGGCCGAGGTGTCCGGTTGATCGGCTTCTGGATTCACTGCGGCACGAAAGGGGGGCTGCCCGTTGCCTGCTGGGGACGGGGGC[G/A]
AACCCTAAGGTGTGGTGCGATCGGTTAGAGGGGGGTTATGCGAAGGGTCCTGTCACGGCCTCTTTCCGGTATGTCGTGGTGGCATGTCGGCGCACGGAAA

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	69.40%	0.10%	5.76%	24.74%	NA
All Indica	2759	63.80%	0.20%	5.65%	30.41%	NA
All Japonica	1512	73.30%	0.10%	7.08%	19.51%	NA
Aus	269	91.80%	0.00%	0.74%	7.43%	NA
Indica I	595	37.00%	0.00%	4.87%	58.15%	NA
Indica II	465	64.50%	0.90%	10.75%	23.87%	NA
Indica III	913	84.10%	0.00%	2.52%	13.36%	NA
Indica Intermediate	786	59.90%	0.10%	6.87%	33.08%	NA
Temperate Japonica	767	93.60%	0.00%	1.43%	4.95%	NA
Tropical Japonica	504	47.60%	0.20%	13.49%	38.69%	NA
Japonica Intermediate	241	62.70%	0.00%	11.62%	25.73%	NA
VI/Aromatic	96	96.90%	0.00%	0.00%	3.12%	NA
Intermediate	90	78.90%	0.00%	7.78%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0826363216	C -> T	LOC_Os08g41770.1	downstream_gene_variant ; 3727.0bp to feature; MODIFIER	silent_mutation	Average:21.967; most accessible tissue: Minghui63 young leaf, score: 47.146	N	N	N	N
vg0826363216	C -> T	LOC_Os08g41760-LOC_Os08g41770	intergenic_region ; MODIFIER	silent_mutation	Average:21.967; most accessible tissue: Minghui63 young leaf, score: 47.146	N	N	N	N
vg0826363216	C -> DEL	N	N	silent_mutation	Average:21.967; most accessible tissue: Minghui63 young leaf, score: 47.146	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0826363216	4.11E-06	NA	mr1611_2	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