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Detailed information for vg0627866244:

Variant ID: vg0627866244 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 27866244
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.04, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

GCTTGGGAGTGAGCTCGAGCGAGCTTCGAGCCTACTTGAGCTTGACAGCTTGACTTGGTGGAACTTCAAAGAACTTACTCTTGTATAAAAGATATTAATG[C/T]
AAATTATCGGTAGTCAAAATTAATGGGTGCTACTCGTTTTGAATGAAGCCTATGCAGCTTTTCTCATGAATTTATGGCTTTGAAACGTTGCAATTAACAA

Reverse complement sequence

TTGTTAATTGCAACGTTTCAAAGCCATAAATTCATGAGAAAAGCTGCATAGGCTTCATTCAAAACGAGTAGCACCCATTAATTTTGACTACCGATAATTT[G/A]
CATTAATATCTTTTATACAAGAGTAAGTTCTTTGAAGTTCCACCAAGTCAAGCTGTCAAGCTCAAGTAGGCTCGAAGCTCGCTCGAGCTCACTCCCAAGC

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	94.00%	5.70%	0.32%	0.00%	NA
All Indica	2759	96.70%	3.00%	0.29%	0.00%	NA
All Japonica	1512	99.30%	0.20%	0.46%	0.00%	NA
Aus	269	36.40%	63.60%	0.00%	0.00%	NA
Indica I	595	98.50%	0.50%	1.01%	0.00%	NA
Indica II	465	97.80%	1.90%	0.22%	0.00%	NA
Indica III	913	95.30%	4.70%	0.00%	0.00%	NA
Indica Intermediate	786	96.30%	3.60%	0.13%	0.00%	NA
Temperate Japonica	767	99.00%	0.10%	0.91%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0627866244	C -> T	LOC_Os06g45980.1	upstream_gene_variant ; 497.0bp to feature; MODIFIER	silent_mutation	Average:65.267; most accessible tissue: Minghui63 flower, score: 78.979	N	N	N	N
vg0627866244	C -> T	LOC_Os06g45970.1	downstream_gene_variant ; 3595.0bp to feature; MODIFIER	silent_mutation	Average:65.267; most accessible tissue: Minghui63 flower, score: 78.979	N	N	N	N
vg0627866244	C -> T	LOC_Os06g45970-LOC_Os06g45980	intergenic_region ; MODIFIER	silent_mutation	Average:65.267; most accessible tissue: Minghui63 flower, score: 78.979	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0627866244	NA	5.27E-10	mr1348	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
vg0627866244	1.74E-06	NA	mr1348_2	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