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Detailed information for vg1009938547:

Variant ID: vg1009938547 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9938547
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAAAGACAGAGGGGACCCCATTTCACTGATTATAATATGTATTCAAGGCTTTACAATTTCTGGGTCTATTACAGCCCATCAGTCAGCCGCTGTCATGCG[T/C]
GCCCGCCTTGCTACTCCGCTTGGCCACTCCCAGCCACCTGATCGGTTCTGGCTGATCTGTGCCAACCATGTGGGTGTTCCATGTTGGCGCCACCTCAGCG

Reverse complement sequence

CGCTGAGGTGGCGCCAACATGGAACACCCACATGGTTGGCACAGATCAGCCAGAACCGATCAGGTGGCTGGGAGTGGCCAAGCGGAGTAGCAAGGCGGGC[A/G]
CGCATGACAGCGGCTGACTGATGGGCTGTAATAGACCCAGAAATTGTAAAGCCTTGAATACATATTATAATCAGTGAAATGGGGTCCCCTCTGTCTTTTG

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	78.50%	21.50%	0.06%	0.00%	NA
All Indica	2759	98.90%	1.10%	0.04%	0.00%	NA
All Japonica	1512	36.40%	63.50%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	98.90%	0.90%	0.22%	0.00%	NA
Indica III	913	98.10%	1.90%	0.00%	0.00%	NA
Indica Intermediate	786	99.10%	0.90%	0.00%	0.00%	NA
Temperate Japonica	767	18.30%	81.70%	0.00%	0.00%	NA
Tropical Japonica	504	55.20%	44.60%	0.20%	0.00%	NA
Japonica Intermediate	241	55.20%	44.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	72.20%	26.70%	1.11%	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
vg1009938547	T -> C	LOC_Os10g19890.1	downstream_gene_variant ; 324.0bp to feature; MODIFIER	silent_mutation	Average:74.728; most accessible tissue: Zhenshan97 panicle, score: 87.451	N	N	N	N
vg1009938547	T -> C	LOC_Os10g19892.1	downstream_gene_variant ; 2731.0bp to feature; MODIFIER	silent_mutation	Average:74.728; most accessible tissue: Zhenshan97 panicle, score: 87.451	N	N	N	N
vg1009938547	T -> C	LOC_Os10g19890-LOC_Os10g19892	intergenic_region ; MODIFIER	silent_mutation	Average:74.728; most accessible tissue: Zhenshan97 panicle, score: 87.451	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009938547	1.83E-06	NA	Grain_width	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
vg1009938547	8.49E-08	3.15E-20	mr1768	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
vg1009938547	NA	8.54E-30	mr1768_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