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Detailed information for vg0915747582:

Variant ID: vg0915747582 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 15747582
Reference Allele: A	Alternative Allele: C,T
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTCTTCTCGTTTAGACATCCAAACTTTAGTATTCCCTTTTTCAACTCATTTTTATCCCCTACTCATTCTCTCTCTGCATGCATTAGGTGGTGTTTGGAT[A/C,T]
CAGGGACTTAACTTTAGTCCCTGTATTTAGACACTAATTTAGAGTATTAAATATAGACTACTTACAAAACTAATTATATAAATGAAAGCTAATTCACGAG

Reverse complement sequence

CTCGTGAATTAGCTTTCATTTATATAATTAGTTTTGTAAGTAGTCTATATTTAATACTCTAAATTAGTGTCTAAATACAGGGACTAAAGTTAAGTCCCTG[T/G,A]
ATCCAAACACCACCTAATGCATGCAGAGAGAGAATGAGTAGGGGATAAAAATGAGTTGAAAAAGGGAATACTAAAGTTTGGATGTCTAAACGAGAAGAAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.90%	34.00%	0.36%	0.02%	T: 4.76%
All Indica	2759	97.40%	1.00%	0.29%	0.00%	T: 1.38%
All Japonica	1512	1.10%	98.30%	0.20%	0.07%	T: 0.26%
Aus	269	32.30%	1.10%	0.00%	0.00%	T: 66.54%
Indica I	595	98.80%	0.80%	0.17%	0.00%	T: 0.17%
Indica II	465	95.90%	2.20%	0.22%	0.00%	T: 1.72%
Indica III	913	98.10%	0.10%	0.33%	0.00%	T: 1.42%
Indica Intermediate	786	96.20%	1.40%	0.38%	0.00%	T: 2.04%
Temperate Japonica	767	0.70%	99.30%	0.00%	0.00%	NA
Tropical Japonica	504	1.60%	97.80%	0.40%	0.00%	T: 0.20%
Japonica Intermediate	241	1.70%	96.30%	0.41%	0.41%	T: 1.24%
VI/Aromatic	96	51.00%	47.90%	0.00%	0.00%	T: 1.04%
Intermediate	90	43.30%	46.70%	6.67%	0.00%	T: 3.33%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0915747582	A -> DEL	N	N	silent_mutation	Average:55.178; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0915747582	A -> T	LOC_Os09g26130-LOC_Os09g26144	intergenic_region ; MODIFIER	silent_mutation	Average:55.178; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0915747582	A -> C	LOC_Os09g26130-LOC_Os09g26144	intergenic_region ; MODIFIER	silent_mutation	Average:55.178; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0915747582	NA	8.38E-31	mr1243	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
vg0915747582	NA	1.57E-12	mr1449	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
vg0915747582	NA	4.19E-36	mr1542	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
vg0915747582	NA	2.22E-34	mr1733	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
vg0915747582	NA	2.33E-86	mr1758	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
vg0915747582	NA	4.48E-53	mr1889	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
vg0915747582	NA	2.20E-38	mr1890	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
vg0915747582	NA	2.50E-65	mr1064_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
vg0915747582	NA	3.37E-12	mr1258_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
vg0915747582	NA	1.52E-45	mr1546_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
vg0915747582	NA	5.21E-19	mr1637_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
vg0915747582	NA	2.12E-62	mr1733_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