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Detailed information for vg0715250362:

Variant ID: vg0715250362 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15250362
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTTTCTCGGACATCTGCAACATGCATCTTCACTTTTGATTGCAATGGCTACTCGACGACAAGAAGCTACAGTTCTCGACTCTATGTTCAGTTGTTTCC[T/C]
AACTAATCAAAGAGTCGGGGGCTACACAAATACAAGGCTCAAAATTTGACAAATTCAACATGTTCGGGAGTTTGGAGTTATCAACCAATCAGCTCGGTTT

Reverse complement sequence

AAACCGAGCTGATTGGTTGATAACTCCAAACTCCCGAACATGTTGAATTTGTCAAATTTTGAGCCTTGTATTTGTGTAGCCCCCGACTCTTTGATTAGTT[A/G]
GGAAACAACTGAACATAGAGTCGAGAACTGTAGCTTCTTGTCGTCGAGTAGCCATTGCAATCAAAAGTGAAGATGCATGTTGCAGATGTCCGAGAAAAAA

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	84.90%	6.50%	4.70%	3.87%	NA
All Indica	2759	97.50%	0.50%	0.25%	1.74%	NA
All Japonica	1512	61.40%	18.70%	13.82%	6.02%	NA
Aus	269	94.80%	0.00%	0.37%	4.83%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.10%	1.70%	0.00%	0.22%	NA
Indica III	913	99.90%	0.00%	0.00%	0.11%	NA
Indica Intermediate	786	92.50%	0.80%	0.89%	5.85%	NA
Temperate Japonica	767	41.90%	26.20%	20.47%	11.47%	NA
Tropical Japonica	504	86.70%	8.70%	4.56%	0.00%	NA
Japonica Intermediate	241	71.00%	15.80%	12.03%	1.24%	NA
VI/Aromatic	96	66.70%	0.00%	2.08%	31.25%	NA
Intermediate	90	84.40%	11.10%	3.33%	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
vg0715250362	T -> DEL	N	N	silent_mutation	Average:34.492; most accessible tissue: Minghui63 young leaf, score: 47.146	N	N	N	N
vg0715250362	T -> C	LOC_Os07g26500-LOC_Os07g26510	intergenic_region ; MODIFIER	silent_mutation	Average:34.492; most accessible tissue: Minghui63 young leaf, score: 47.146	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715250362	1.14E-06	NA	mr1415	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
vg0715250362	1.14E-06	NA	mr1567	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