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Detailed information for vg0139349964:

Variant ID: vg0139349964 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 39349964
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTGGGTTATTTGAGAGCTAAGTTCCCTATGCGATAGGCTAAGTTTCTACTTTAAACCTATTCGATAGGCTAACCGGATGTAGATGCCGGGTAAAAAATA[T/C]
CCTCCTATGTGATAGGCTAAGTTTCTACTTTAAACCTATTCGATAAGCTAACCGGATGTAGATGCCGGGTAAAAAATATCCTTCTCTCTTAAAAAAAGAG

Reverse complement sequence

CTCTTTTTTTAAGAGAGAAGGATATTTTTTACCCGGCATCTACATCCGGTTAGCTTATCGAATAGGTTTAAAGTAGAAACTTAGCCTATCACATAGGAGG[A/G]
TATTTTTTACCCGGCATCTACATCCGGTTAGCCTATCGAATAGGTTTAAAGTAGAAACTTAGCCTATCGCATAGGGAACTTAGCTCTCAAATAACCCAAT

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	33.20%	0.40%	1.02%	65.36%	NA
All Indica	2759	2.60%	0.70%	1.01%	95.76%	NA
All Japonica	1512	93.50%	0.10%	0.07%	6.35%	NA
Aus	269	3.30%	0.00%	4.46%	92.19%	NA
Indica I	595	2.70%	0.70%	0.67%	95.97%	NA
Indica II	465	1.10%	1.10%	0.43%	97.42%	NA
Indica III	913	1.20%	0.40%	1.10%	97.26%	NA
Indica Intermediate	786	5.00%	0.60%	1.53%	92.88%	NA
Temperate Japonica	767	98.60%	0.10%	0.00%	1.30%	NA
Tropical Japonica	504	87.10%	0.00%	0.20%	12.70%	NA
Japonica Intermediate	241	90.90%	0.00%	0.00%	9.13%	NA
VI/Aromatic	96	32.30%	1.00%	4.17%	62.50%	NA
Intermediate	90	48.90%	0.00%	3.33%	47.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0139349964	T -> DEL	N	N	silent_mutation	Average:49.777; most accessible tissue: Zhenshan97 panicle, score: 82.336	N	N	N	N
vg0139349964	T -> C	LOC_Os01g67700.1	downstream_gene_variant ; 3878.0bp to feature; MODIFIER	silent_mutation	Average:49.777; most accessible tissue: Zhenshan97 panicle, score: 82.336	N	N	N	N
vg0139349964	T -> C	LOC_Os01g67710.1	intron_variant ; MODIFIER	silent_mutation	Average:49.777; most accessible tissue: Zhenshan97 panicle, score: 82.336	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0139349964	NA	3.59E-10	Grain_weight	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
vg0139349964	NA	2.26E-06	mr1028	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
vg0139349964	NA	3.60E-07	mr1453	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