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Detailed information for vg1011720271:

Variant ID: vg1011720271 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 11720271
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTTAAAACCACTTCGATATAGAAAGTTTTTTTTTAAAAAAATATACCATTTAGTAGGCGAGGAAAATAGCTCACTCCATTTATACAAATGAAAGTAGC[G/T]
TTAGGCTGCGTCTGGCAGTAGCACAAAGATTAAAACTCTCTTGTTTTTGTGCGCGCGCTTTTAGAAAAAGTTGCTTGACAAAATCAAATTAATTTTTTTT

Reverse complement sequence

AAAAAAAATTAATTTGATTTTGTCAAGCAACTTTTTCTAAAAGCGCGCGCACAAAAACAAGAGAGTTTTAATCTTTGTGCTACTGCCAGACGCAGCCTAA[C/A]
GCTACTTTCATTTGTATAAATGGAGTGAGCTATTTTCCTCGCCTACTAAATGGTATATTTTTTTAAAAAAAAACTTTCTATATCGAAGTGGTTTTAAAAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.80%	5.50%	0.17%	0.53%	NA
All Indica	2759	99.90%	0.00%	0.14%	0.00%	NA
All Japonica	1512	81.20%	17.10%	0.20%	1.52%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.00%	0.43%	0.00%	NA
Indica III	913	99.80%	0.00%	0.22%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	80.80%	16.90%	0.13%	2.09%	NA
Tropical Japonica	504	76.20%	22.60%	0.20%	0.99%	NA
Japonica Intermediate	241	92.90%	5.80%	0.41%	0.83%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	93.30%	4.40%	1.11%	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
vg1011720271	G -> T	LOC_Os10g22580.1	upstream_gene_variant ; 2404.0bp to feature; MODIFIER	silent_mutation	Average:56.537; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N
vg1011720271	G -> T	LOC_Os10g22590.1	upstream_gene_variant ; 3148.0bp to feature; MODIFIER	silent_mutation	Average:56.537; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N
vg1011720271	G -> T	LOC_Os10g22580-LOC_Os10g22590	intergenic_region ; MODIFIER	silent_mutation	Average:56.537; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N
vg1011720271	G -> DEL	N	N	silent_mutation	Average:56.537; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1011720271	3.04E-06	NA	mr1771	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