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Detailed information for vg0528175027:

Variant ID: vg0528175027 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 28175027
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCAGGCCCGTGTGGCCGTTTGAAAGTTGTTGGCTGGGTGCCAACCTTGAATCAATTCAAAGACTGATATATTGCACATACTCCGACCGGGCGTGATGCA[C/T]
TGTCTCATCCGTGTCGTTTGAGAAGCACTCACTTAGTGGTTTCAAAAAGGAGTTTAAATAAAATTAATTGCAAAAACAACAGTCTTTCCTTGAAGCCTGC

Reverse complement sequence

GCAGGCTTCAAGGAAAGACTGTTGTTTTTGCAATTAATTTTATTTAAACTCCTTTTTGAAACCACTAAGTGAGTGCTTCTCAAACGACACGGATGAGACA[G/A]
TGCATCACGCCCGGTCGGAGTATGTGCAATATATCAGTCTTTGAATTGATTCAAGGTTGGCACCCAGCCAACAACTTTCAAACGGCCACACGGGCCTGAC

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	99.80%	0.20%	0.06%	0.00%	NA
All Indica	2759	99.70%	0.30%	0.04%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	98.90%	0.40%	0.74%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.50%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0528175027	C -> T	LOC_Os05g49120.1	upstream_gene_variant ; 1550.0bp to feature; MODIFIER	N	Average:42.52; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0528175027	C -> T	LOC_Os05g49120.2	upstream_gene_variant ; 1550.0bp to feature; MODIFIER	N	Average:42.52; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0528175027	C -> T	LOC_Os05g49110-LOC_Os05g49120	intergenic_region ; MODIFIER	N	Average:42.52; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0528175027	4.56E-06	NA	mr1212_2	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