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Detailed information for vg0816175621:

Variant ID: vg0816175621 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16175621
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACTGCCCGCTGCCTTGCGAGGAGTGGGGGTTGTGAAACCTGAGGTGTGGTGTGCTTGGTTAGAGGGGGTTATGCGAAGGGTCCTATCACAGCCTCTATC[T/C]
GGTATGTCGTGGTGGCATGTCGGCGCACGGGAACGTGTCGTGGGGCTGTGTCTTGTGGGTACAGTTGTACACCTCTGATCAGAGTAAAACTATTCGAATA

Reverse complement sequence

TATTCGAATAGTTTTACTCTGATCAGAGGTGTACAACTGTACCCACAAGACACAGCCCCACGACACGTTCCCGTGCGCCGACATGCCACCACGACATACC[A/G]
GATAGAGGCTGTGATAGGACCCTTCGCATAACCCCCTCTAACCAAGCACACCACACCTCAGGTTTCACAACCCCCACTCCTCGCAAGGCAGCGGGCAGTC

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	89.50%	3.60%	0.42%	6.45%	NA
All Indica	2759	98.10%	0.30%	0.33%	1.27%	NA
All Japonica	1512	72.00%	10.70%	0.60%	16.73%	NA
Aus	269	95.90%	0.00%	0.00%	4.09%	NA
Indica I	595	97.50%	1.30%	0.50%	0.67%	NA
Indica II	465	97.00%	0.00%	0.65%	2.37%	NA
Indica III	913	98.80%	0.00%	0.22%	0.99%	NA
Indica Intermediate	786	98.50%	0.00%	0.13%	1.40%	NA
Temperate Japonica	767	82.00%	16.90%	0.13%	0.91%	NA
Tropical Japonica	504	52.20%	4.40%	1.59%	41.87%	NA
Japonica Intermediate	241	81.30%	4.10%	0.00%	14.52%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	91.10%	2.20%	2.22%	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
vg0816175621	T -> C	LOC_Os08g26580.1	downstream_gene_variant ; 2524.0bp to feature; MODIFIER	silent_mutation	Average:8.852; most accessible tissue: Callus, score: 16.609	N	N	N	N
vg0816175621	T -> C	LOC_Os08g26560-LOC_Os08g26580	intergenic_region ; MODIFIER	silent_mutation	Average:8.852; most accessible tissue: Callus, score: 16.609	N	N	N	N
vg0816175621	T -> DEL	N	N	silent_mutation	Average:8.852; most accessible tissue: Callus, score: 16.609	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816175621	1.42E-07	1.42E-07	mr1525_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