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Detailed information for vg0614871126:

Variant ID: vg0614871126 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 14871126
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

GCTCGCGAACCGGTCCTTAATTGTCATGAGCACGACCTTCAAAACCATGTGCTCACAACCCACCATTAATCATATTTTAATTATCAATTAATTATCATAA[C/T]
ACGATTGACCATCGTGAGCTACCATTAAATATAACCGTAAGTAATAGTGAAGCATAATTTATCCCATTAATGAGCTAATGTTTCTAAGCATGACTAATCA

Reverse complement sequence

TGATTAGTCATGCTTAGAAACATTAGCTCATTAATGGGATAAATTATGCTTCACTATTACTTACGGTTATATTTAATGGTAGCTCACGATGGTCAATCGT[G/A]
TTATGATAATTAATTGATAATTAAAATATGATTAATGGTGGGTTGTGAGCACATGGTTTTGAAGGTCGTGCTCATGACAATTAAGGACCGGTTCGCGAGC

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	78.10%	2.70%	11.66%	7.53%	NA
All Indica	2759	67.10%	3.20%	17.40%	12.32%	NA
All Japonica	1512	94.10%	2.40%	3.17%	0.33%	NA
Aus	269	92.20%	0.70%	5.20%	1.86%	NA
Indica I	595	91.30%	0.80%	6.39%	1.51%	NA
Indica II	465	79.80%	2.20%	11.40%	6.67%	NA
Indica III	913	39.40%	5.80%	27.93%	26.83%	NA
Indica Intermediate	786	73.50%	2.40%	17.05%	7.00%	NA
Temperate Japonica	767	98.00%	0.90%	0.91%	0.13%	NA
Tropical Japonica	504	87.10%	5.20%	6.94%	0.79%	NA
Japonica Intermediate	241	96.30%	1.20%	2.49%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	82.20%	1.10%	10.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0614871126	C -> T	LOC_Os06g25390.1	upstream_gene_variant ; 4156.0bp to feature; MODIFIER	silent_mutation	Average:31.094; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0614871126	C -> T	LOC_Os06g25390-LOC_Os06g25410	intergenic_region ; MODIFIER	silent_mutation	Average:31.094; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0614871126	C -> DEL	N	N	silent_mutation	Average:31.094; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0614871126	6.73E-08	6.71E-08	mr1197_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
vg0614871126	9.30E-06	2.67E-07	mr1197_2	Ind_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