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Detailed information for vg0417133455:

Variant ID: vg0417133455 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 17133455
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCTATCACCCATGACAGTAAGGGACAAATCCATCACACACATGAGCAAATTTTTCTAAGGGGAGGAGGGAAGAAGGGGGAGAGGGGTGTACCTCTGCGT[T/C]
GGGCCATCCTCCTCTCCTCCACATCCGCCTTGCCGCCGCGCACCGCTGCCCCTCTTTACCTCGCCGCCGCACCGTGCCACTGTCGCTGCAAGAATCATCG

Reverse complement sequence

CGATGATTCTTGCAGCGACAGTGGCACGGTGCGGCGGCGAGGTAAAGAGGGGCAGCGGTGCGCGGCGGCAAGGCGGATGTGGAGGAGAGGAGGATGGCCC[A/G]
ACGCAGAGGTACACCCCTCTCCCCCTTCTTCCCTCCTCCCCTTAGAAAAATTTGCTCATGTGTGTGATGGATTTGTCCCTTACTGTCATGGGTGATAGAT

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	95.90%	3.70%	0.08%	0.40%	NA
All Indica	2759	98.80%	0.90%	0.04%	0.22%	NA
All Japonica	1512	99.80%	0.10%	0.07%	0.07%	NA
Aus	269	50.60%	46.50%	0.00%	2.97%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	98.20%	1.30%	0.00%	0.44%	NA
Indica Intermediate	786	98.00%	1.70%	0.13%	0.25%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.00%	0.20%	0.20%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	77.10%	16.70%	2.08%	4.17%	NA
Intermediate	90	93.30%	6.70%	0.00%	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
vg0417133455	T -> C	LOC_Os04g28910.1	upstream_gene_variant ; 3449.0bp to feature; MODIFIER	silent_mutation	Average:59.216; most accessible tissue: Zhenshan97 flag leaf, score: 79.71	N	N	N	N
vg0417133455	T -> C	LOC_Os04g28900-LOC_Os04g28910	intergenic_region ; MODIFIER	silent_mutation	Average:59.216; most accessible tissue: Zhenshan97 flag leaf, score: 79.71	N	N	N	N
vg0417133455	T -> DEL	N	N	silent_mutation	Average:59.216; most accessible tissue: Zhenshan97 flag leaf, score: 79.71	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0417133455	4.02E-07	NA	mr1855	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