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Detailed information for vg0116370525:

Variant ID: vg0116370525 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 16370525
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCAACTGTGCAGATTGCCGGTATTAATATATTGTTTGAATATAATGCTCAGATCTACTTTAGATATGCCATTCAGAGTTCCCTCAATTAATAATGGTGG[T/C]
GCTTGTGTGTTTGGATGGTTATGGATTATTATATTATATTTAATATTGTTGAAAACTCAAAATGAGTAACTAAAGTGAAGTAACATGTGATGCAATGTAC

Reverse complement sequence

GTACATTGCATCACATGTTACTTCACTTTAGTTACTCATTTTGAGTTTTCAACAATATTAAATATAATATAATAATCCATAACCATCCAAACACACAAGC[A/G]
CCACCATTATTAATTGAGGGAACTCTGAATGGCATATCTAAAGTAGATCTGAGCATTATATTCAAACAATATATTAATACCGGCAATCTGCACAGTTGAT

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	87.60%	9.90%	2.52%	0.00%	NA
All Indica	2759	99.70%	0.30%	0.00%	0.00%	NA
All Japonica	1512	62.50%	29.90%	7.61%	0.00%	NA
Aus	269	98.50%	0.70%	0.74%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	37.30%	51.40%	11.34%	0.00%	NA
Tropical Japonica	504	96.20%	0.60%	3.17%	0.00%	NA
Japonica Intermediate	241	72.20%	22.80%	4.98%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	6.70%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0116370525	T -> C	LOC_Os01g29220.1	downstream_gene_variant ; 668.0bp to feature; MODIFIER	silent_mutation	Average:48.003; most accessible tissue: Callus, score: 67.104	N	N	N	N
vg0116370525	T -> C	LOC_Os01g29220-LOC_Os01g29230	intergenic_region ; MODIFIER	silent_mutation	Average:48.003; most accessible tissue: Callus, score: 67.104	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0116370525	NA	1.49E-07	mr1002	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
vg0116370525	NA	2.10E-06	mr1013	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
vg0116370525	NA	1.72E-06	mr1031	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
vg0116370525	NA	5.49E-13	mr1034	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
vg0116370525	NA	4.99E-07	mr1034	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
vg0116370525	NA	9.77E-06	mr1077	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
vg0116370525	5.82E-06	5.55E-07	mr1170	Jap_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
vg0116370525	NA	3.06E-07	mr1202	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
vg0116370525	NA	1.11E-07	mr1252	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
vg0116370525	NA	5.36E-06	mr1548	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
vg0116370525	NA	2.42E-06	mr1555	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
vg0116370525	NA	7.63E-07	mr1576	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
vg0116370525	NA	1.26E-06	mr1013_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