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Detailed information for vg0715040245:

Variant ID: vg0715040245 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15040245
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.79, C: 0.21, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTATCTTTTTAGCTTTTTTCATCGTATACGTACGTTCATTGTTTTTTTTTTCAAACGAACAGTTCCGACAGGTATATCTTTTGTTGTACGTACATACT[T/C]
AAAATTTTCTAGTAAGCGATTCTCAACTATCTGAATTCCCCAGAGTTGCCACATGAGTTTCAAAATGGCAAACTATTCATTTACGAATGGCACCTAGCAG

Reverse complement sequence

CTGCTAGGTGCCATTCGTAAATGAATAGTTTGCCATTTTGAAACTCATGTGGCAACTCTGGGGAATTCAGATAGTTGAGAATCGCTTACTAGAAAATTTT[A/G]
AGTATGTACGTACAACAAAAGATATACCTGTCGGAACTGTTCGTTTGAAAAAAAAAACAATGAACGTACGTATACGATGAAAAAAGCTAAAAAGATAAAA

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	57.30%	40.50%	0.28%	1.90%	NA
All Indica	2759	40.30%	57.80%	0.22%	1.67%	NA
All Japonica	1512	94.00%	5.80%	0.00%	0.20%	NA
Aus	269	24.90%	70.30%	1.86%	2.97%	NA
Indica I	595	49.40%	44.50%	0.34%	5.71%	NA
Indica II	465	20.90%	78.90%	0.22%	0.00%	NA
Indica III	913	33.30%	66.50%	0.11%	0.11%	NA
Indica Intermediate	786	53.20%	45.20%	0.25%	1.40%	NA
Temperate Japonica	767	89.00%	11.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	1.20%	0.00%	1.24%	NA
VI/Aromatic	96	51.00%	14.60%	1.04%	33.33%	NA
Intermediate	90	64.40%	33.30%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0715040245	T -> DEL	N	N	silent_mutation	Average:41.291; most accessible tissue: Minghui63 flag leaf, score: 65.44	N	N	N	N
vg0715040245	T -> C	LOC_Os07g26160.1	upstream_gene_variant ; 139.0bp to feature; MODIFIER	silent_mutation	Average:41.291; most accessible tissue: Minghui63 flag leaf, score: 65.44	N	N	N	N
vg0715040245	T -> C	LOC_Os07g26150-LOC_Os07g26160	intergenic_region ; MODIFIER	silent_mutation	Average:41.291; most accessible tissue: Minghui63 flag leaf, score: 65.44	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715040245	NA	2.35E-06	mr1169	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
vg0715040245	3.77E-06	3.77E-06	mr1880	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
vg0715040245	NA	9.59E-07	mr1161_2	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