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Detailed information for vg0619726119:

Variant ID: vg0619726119 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19726119
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

CGGGGCGGACGGTGGATTTGGGTGGTATCCGGGAAAGGCTAGTACCGTCCCCGGTCAATTAAGGACCGAGCCATGAAGTTAAGTACGAAACGACCCCGTA[C/T]
AACCACACTTCTCGAATGGGGATAGACCTAGCGGAGTAAATAGCCGAGCGGAGGCAGTATCCATGCATAGTGGTTTCTCATGTGTAAGGCAGGGGCTCTA

Reverse complement sequence

TAGAGCCCCTGCCTTACACATGAGAAACCACTATGCATGGATACTGCCTCCGCTCGGCTATTTACTCCGCTAGGTCTATCCCCATTCGAGAAGTGTGGTT[G/A]
TACGGGGTCGTTTCGTACTTAACTTCATGGCTCGGTCCTTAATTGACCGGGGACGGTACTAGCCTTTCCCGGATACCACCCAAATCCACCGTCCGCCCCG

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	48.60%	17.90%	7.13%	26.41%	NA
All Indica	2759	30.40%	25.70%	10.40%	33.53%	NA
All Japonica	1512	81.20%	0.10%	1.12%	17.66%	NA
Aus	269	28.60%	47.60%	10.04%	13.75%	NA
Indica I	595	8.20%	37.60%	6.22%	47.90%	NA
Indica II	465	45.60%	9.50%	9.46%	35.48%	NA
Indica III	913	39.00%	29.20%	12.27%	19.50%	NA
Indica Intermediate	786	28.20%	22.00%	11.96%	37.79%	NA
Temperate Japonica	767	73.40%	0.00%	0.91%	25.68%	NA
Tropical Japonica	504	91.10%	0.20%	1.39%	7.34%	NA
Japonica Intermediate	241	85.10%	0.00%	1.24%	13.69%	NA
VI/Aromatic	96	93.80%	2.10%	3.12%	1.04%	NA
Intermediate	90	71.10%	5.60%	3.33%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0619726119	C -> T	LOC_Os06g33900.1	upstream_gene_variant ; 4268.0bp to feature; MODIFIER	silent_mutation	Average:8.777; most accessible tissue: Minghui63 root, score: 15.664	N	N	N	N
vg0619726119	C -> T	LOC_Os06g33910.1	upstream_gene_variant ; 1499.0bp to feature; MODIFIER	silent_mutation	Average:8.777; most accessible tissue: Minghui63 root, score: 15.664	N	N	N	N
vg0619726119	C -> T	LOC_Os06g33910-LOC_Os06g33930	intergenic_region ; MODIFIER	silent_mutation	Average:8.777; most accessible tissue: Minghui63 root, score: 15.664	N	N	N	N
vg0619726119	C -> DEL	N	N	silent_mutation	Average:8.777; most accessible tissue: Minghui63 root, score: 15.664	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619726119	4.69E-06	NA	mr1509	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
vg0619726119	NA	3.53E-06	mr1646	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
vg0619726119	NA	6.12E-06	mr1835	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