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Detailed information for vg0913504136:

Variant ID: vg0913504136 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 13504136
Reference Allele: T	Alternative Allele: C,G
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCATCGACGATCTATTCCGGTTTCGTAAGTTTTACGTTTATGTTTGGTTTTGGTATTAACTTGTGATTGTTCGTGTTGCTGTGATTTTGTTCAAGTTAAT[T/C,G]
CATCCAAAACCTTTCTAATACTTCATAGATCACATCTGGAAAGTTTCGTTGATTGGTTCTGGTTAGATTTGAATTTGCTTAACTTTTAGGTTTTGTTCAG

Reverse complement sequence

CTGAACAAAACCTAAAAGTTAAGCAAATTCAAATCTAACCAGAACCAATCAACGAAACTTTCCAGATGTGATCTATGAAGTATTAGAAAGGTTTTGGATG[A/G,C]
ATTAACTTGAACAAAATCACAGCAACACGAACAATCACAAGTTAATACCAAAACCAAACATAAACGTAAAACTTACGAAACCGGAATAGATCGTCGATGC

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	38.60%	0.80%	3.72%	56.81%	G: 0.04%
All Indica	2759	11.50%	1.40%	2.14%	84.81%	G: 0.07%
All Japonica	1512	92.00%	0.00%	1.92%	6.08%	NA
Aus	269	17.80%	0.00%	21.19%	60.97%	NA
Indica I	595	21.20%	1.20%	2.18%	75.46%	NA
Indica II	465	17.20%	0.20%	1.72%	80.65%	G: 0.22%
Indica III	913	2.50%	1.90%	2.74%	92.88%	NA
Indica Intermediate	786	11.30%	1.90%	1.65%	84.99%	G: 0.13%
Temperate Japonica	767	96.60%	0.00%	0.39%	3.00%	NA
Tropical Japonica	504	84.10%	0.00%	4.56%	11.31%	NA
Japonica Intermediate	241	93.80%	0.00%	1.24%	4.98%	NA
VI/Aromatic	96	17.70%	0.00%	31.25%	51.04%	NA
Intermediate	90	54.40%	0.00%	1.11%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0913504136	T -> G	LOC_Os09g22350.1	upstream_gene_variant ; 1862.0bp to feature; MODIFIER	silent_mutation	Average:22.616; most accessible tissue: Callus, score: 48.093	N	N	N	N
vg0913504136	T -> G	LOC_Os09g22340-LOC_Os09g22350	intergenic_region ; MODIFIER	silent_mutation	Average:22.616; most accessible tissue: Callus, score: 48.093	N	N	N	N
vg0913504136	T -> DEL	N	N	silent_mutation	Average:22.616; most accessible tissue: Callus, score: 48.093	N	N	N	N
vg0913504136	T -> C	LOC_Os09g22350.1	upstream_gene_variant ; 1862.0bp to feature; MODIFIER	silent_mutation	Average:22.616; most accessible tissue: Callus, score: 48.093	N	N	N	N
vg0913504136	T -> C	LOC_Os09g22340-LOC_Os09g22350	intergenic_region ; MODIFIER	silent_mutation	Average:22.616; most accessible tissue: Callus, score: 48.093	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0913504136	2.33E-06	NA	Grain_weight	Ind_All	YES	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
vg0913504136	NA	2.38E-07	mr1527_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