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Detailed information for vg0615019600:

Variant ID: vg0615019600 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 15019600
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCTAGATTGAGTGGAGAAGGCAAGAAACACTTGTGAGAGTCTAGCAACAGCTCTAGGTTTGAAAAGTGAAAGTGGAATGGCCAAAGAACGAGCTGGAAA[C/T]
GAGCTGTATATGTATAACGGCTAGGTGACGTCATCTAGCTGTTACTCACAAATTTGAACTGGAGACTAGACAGGAAGTTCCGGACCTGTAGGATATTATA

Reverse complement sequence

TATAATATCCTACAGGTCCGGAACTTCCTGTCTAGTCTCCAGTTCAAATTTGTGAGTAACAGCTAGATGACGTCACCTAGCCGTTATACATATACAGCTC[G/A]
TTTCCAGCTCGTTCTTTGGCCATTCCACTTTCACTTTTCAAACCTAGAGCTGTTGCTAGACTCTCACAAGTGTTTCTTGCCTTCTCCACTCAATCTAGAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.10%	36.90%	9.78%	3.22%	NA
All Indica	2759	76.70%	4.00%	15.98%	3.30%	NA
All Japonica	1512	8.40%	91.10%	0.40%	0.13%	NA
Aus	269	27.90%	69.50%	1.86%	0.74%	NA
Indica I	595	61.20%	7.20%	24.71%	6.89%	NA
Indica II	465	66.00%	1.90%	26.02%	6.02%	NA
Indica III	913	94.00%	0.50%	4.71%	0.77%	NA
Indica Intermediate	786	74.70%	6.90%	16.54%	1.91%	NA
Temperate Japonica	767	3.10%	96.50%	0.39%	0.00%	NA
Tropical Japonica	504	17.10%	82.30%	0.20%	0.40%	NA
Japonica Intermediate	241	7.10%	92.10%	0.83%	0.00%	NA
VI/Aromatic	96	16.70%	25.00%	3.12%	55.21%	NA
Intermediate	90	40.00%	47.80%	7.78%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0615019600	C -> T	LOC_Os06g25710.1	upstream_gene_variant ; 963.0bp to feature; MODIFIER	silent_mutation	Average:18.593; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0615019600	C -> T	LOC_Os06g25720.1	downstream_gene_variant ; 622.0bp to feature; MODIFIER	silent_mutation	Average:18.593; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0615019600	C -> T	LOC_Os06g25710-LOC_Os06g25720	intergenic_region ; MODIFIER	silent_mutation	Average:18.593; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0615019600	C -> DEL	N	N	silent_mutation	Average:18.593; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0615019600	6.33E-06	NA	mr1176	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
vg0615019600	1.27E-07	2.75E-08	mr1719	Ind_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
vg0615019600	NA	1.09E-06	mr1548_2	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