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Detailed information for vg0630243903:

Variant ID: vg0630243903 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 30243903
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTCAGCCATTCAAATATCAAAATACTGAAATTAACGAGGAAATAACTTGCGAACTTTCGAAAGAACAATAAGGAAACAATTTATGCAGTGCCATTGTTC[A/T]
GTATCAGTGGAAAACTCTGCAGATACTCTATCATAAACTACAGTCGCAATTGAATGATTTGATTTTGTTACAGAACAACAGAGTTGAGGTTCATATACCT

Reverse complement sequence

AGGTATATGAACCTCAACTCTGTTGTTCTGTAACAAAATCAAATCATTCAATTGCGACTGTAGTTTATGATAGAGTATCTGCAGAGTTTTCCACTGATAC[T/A]
GAACAATGGCACTGCATAAATTGTTTCCTTATTGTTCTTTCGAAAGTTCGCAAGTTATTTCCTCGTTAATTTCAGTATTTTGATATTTGAATGGCTGAGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	25.80%	3.20%	3.81%	67.18%	NA
All Indica	2759	3.80%	0.10%	3.41%	92.68%	NA
All Japonica	1512	61.60%	7.90%	1.46%	29.10%	NA
Aus	269	55.40%	0.00%	20.45%	24.16%	NA
Indica I	595	3.40%	0.00%	3.19%	93.45%	NA
Indica II	465	2.20%	0.20%	1.29%	96.34%	NA
Indica III	913	3.40%	0.00%	5.15%	91.46%	NA
Indica Intermediate	786	5.70%	0.10%	2.80%	91.35%	NA
Temperate Japonica	767	91.50%	1.20%	0.26%	7.04%	NA
Tropical Japonica	504	27.40%	7.70%	3.57%	61.31%	NA
Japonica Intermediate	241	37.80%	29.50%	0.83%	31.95%	NA
VI/Aromatic	96	8.30%	28.10%	5.21%	58.33%	NA
Intermediate	90	26.70%	5.60%	4.44%	63.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0630243903	A -> T	LOC_Os06g49950.1	upstream_gene_variant ; 732.0bp to feature; MODIFIER	silent_mutation	Average:7.064; most accessible tissue: Callus, score: 30.064	N	N	N	N
vg0630243903	A -> T	LOC_Os06g49940-LOC_Os06g49950	intergenic_region ; MODIFIER	silent_mutation	Average:7.064; most accessible tissue: Callus, score: 30.064	N	N	N	N
vg0630243903	A -> DEL	N	N	silent_mutation	Average:7.064; most accessible tissue: Callus, score: 30.064	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0630243903	2.15E-06	2.15E-06	mr1009	Jap_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