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Detailed information for vg0101001636:

Variant ID: vg0101001636 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 1001636
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.02, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

TGAAGTCCTTGTCCAATTTATGAACCAGAATCTGGTGGAAATGTCACAGGAGGATCATTATGCAGCGCAATTAACCGCGATGTAGAATAGATTAACTGTG[C/T]
GAGTATAAGACTCATCATGGATTTGAGCGCAGTAACTCCAAGATTCAAATAGAAAAAGAACAAATCGTAGAAAAGTTACCTTTGTTAATTCCAACTAGGA

Reverse complement sequence

TCCTAGTTGGAATTAACAAAGGTAACTTTTCTACGATTTGTTCTTTTTCTATTTGAATCTTGGAGTTACTGCGCTCAAATCCATGATGAGTCTTATACTC[G/A]
CACAGTTAATCTATTCTACATCGCGGTTAATTGCGCTGCATAATGATCCTCCTGTGACATTTCCACCAGATTCTGGTTCATAAATTGGACAAGGACTTCA

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	68.90%	30.60%	0.17%	0.32%	NA
All Indica	2759	93.70%	5.80%	0.07%	0.36%	NA
All Japonica	1512	31.20%	68.40%	0.20%	0.20%	NA
Aus	269	50.60%	49.10%	0.00%	0.37%	NA
Indica I	595	98.70%	1.00%	0.00%	0.34%	NA
Indica II	465	95.70%	4.10%	0.22%	0.00%	NA
Indica III	913	96.90%	2.70%	0.11%	0.22%	NA
Indica Intermediate	786	85.10%	14.10%	0.00%	0.76%	NA
Temperate Japonica	767	6.60%	93.00%	0.39%	0.00%	NA
Tropical Japonica	504	77.40%	22.00%	0.00%	0.60%	NA
Japonica Intermediate	241	12.90%	87.10%	0.00%	0.00%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	56.70%	38.90%	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
vg0101001636	C -> T	LOC_Os01g02830.1	upstream_gene_variant ; 4374.0bp to feature; MODIFIER	silent_mutation	Average:70.509; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N
vg0101001636	C -> T	LOC_Os01g02840.1	downstream_gene_variant ; 639.0bp to feature; MODIFIER	silent_mutation	Average:70.509; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N
vg0101001636	C -> T	LOC_Os01g02860.1	downstream_gene_variant ; 823.0bp to feature; MODIFIER	silent_mutation	Average:70.509; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N
vg0101001636	C -> T	LOC_Os01g02850.1	intron_variant ; MODIFIER	silent_mutation	Average:70.509; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N
vg0101001636	C -> DEL	N	N	silent_mutation	Average:70.509; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0101001636	NA	6.72E-07	Awn_length	Ind_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0101001636	NA	6.60E-08	mr1518	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
vg0101001636	NA	2.45E-07	mr1551	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
vg0101001636	1.14E-06	1.14E-06	mr1722	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