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Detailed information for vg0713891677:

Variant ID: vg0713891677 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 13891677
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

ATACGAGTACGACCGCAATTCTCGTATGGGCATAGACCTAGCTGATTAAGTTATCTAGCAAAGGTGGTACCTCTGTATTGTGGTTCTTCTTAAGTCCTCG[T/C]
GCAGGAGGCAAACTTACGCCGAGCAGGGCGATTGTAATATTTACCGAGGCGCAGGTAAATATTTGAGATAAATTGTGATATCACAAACTGTGTGTATTGT

Reverse complement sequence

ACAATACACACAGTTTGTGATATCACAATTTATCTCAAATATTTACCTGCGCCTCGGTAAATATTACAATCGCCCTGCTCGGCGTAAGTTTGCCTCCTGC[A/G]
CGAGGACTTAAGAAGAACCACAATACAGAGGTACCACCTTTGCTAGATAACTTAATCAGCTAGGTCTATGCCCATACGAGAATTGCGGTCGTACTCGTAT

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	74.50%	17.50%	2.90%	5.10%	NA
All Indica	2759	87.90%	6.90%	3.41%	1.85%	NA
All Japonica	1512	46.80%	40.30%	1.39%	11.57%	NA
Aus	269	88.10%	2.20%	7.43%	2.23%	NA
Indica I	595	73.10%	16.30%	7.39%	3.19%	NA
Indica II	465	96.10%	2.60%	1.08%	0.22%	NA
Indica III	913	97.80%	0.90%	0.77%	0.55%	NA
Indica Intermediate	786	82.60%	9.30%	4.83%	3.31%	NA
Temperate Japonica	767	26.70%	61.10%	1.69%	10.43%	NA
Tropical Japonica	504	83.10%	10.90%	0.60%	5.36%	NA
Japonica Intermediate	241	34.40%	35.30%	2.07%	28.22%	NA
VI/Aromatic	96	91.70%	3.10%	0.00%	5.21%	NA
Intermediate	90	70.00%	23.30%	2.22%	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
vg0713891677	T -> DEL	N	N	silent_mutation	Average:48.237; most accessible tissue: Minghui63 flag leaf, score: 68.16	N	N	N	N
vg0713891677	T -> C	LOC_Os07g24400.1	upstream_gene_variant ; 1140.0bp to feature; MODIFIER	silent_mutation	Average:48.237; most accessible tissue: Minghui63 flag leaf, score: 68.16	N	N	N	N
vg0713891677	T -> C	LOC_Os07g24390.1	downstream_gene_variant ; 3784.0bp to feature; MODIFIER	silent_mutation	Average:48.237; most accessible tissue: Minghui63 flag leaf, score: 68.16	N	N	N	N
vg0713891677	T -> C	LOC_Os07g24390-LOC_Os07g24400	intergenic_region ; MODIFIER	silent_mutation	Average:48.237; most accessible tissue: Minghui63 flag leaf, score: 68.16	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0713891677	4.48E-07	4.46E-07	mr1703	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