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Detailed information for vg1021216544:

Variant ID: vg1021216544 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 21216544
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTGACAAGTATCGACGGTCGCCTTTAAACTTAAAATTTGAGTAACTTCTTGGGTAACACTTGGTTTACAAAATCTTTGGAAAACCCGACGCCTGGGTCG[G/T]
TGCCTTGTGAAAGAAAATGAGTTTTAAAAATGAAACTCGCGACACAAGGCCATTCCTGGGTGGAATACTTGTGCGGTCGCATTTAAGGACCGATTCCTTC

Reverse complement sequence

GAAGGAATCGGTCCTTAAATGCGACCGCACAAGTATTCCACCCAGGAATGGCCTTGTGTCGCGAGTTTCATTTTTAAAACTCATTTTCTTTCACAAGGCA[C/A]
CGACCCAGGCGTCGGGTTTTCCAAAGATTTTGTAAACCAAGTGTTACCCAAGAAGTTACTCAAATTTTAAGTTTAAAGGCGACCGTCGATACTTGTCACG

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	90.70%	9.30%	0.00%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	71.40%	28.60%	0.00%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	49.40%	50.60%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	82.60%	17.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg1021216544	G -> T	LOC_Os10g39700.1	upstream_gene_variant ; 2941.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1021216544	G -> T	LOC_Os10g39690-LOC_Os10g39700	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1021216544	1.25E-06	NA	mr1765	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
vg1021216544	NA	2.99E-06	mr1765	Jap_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