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Detailed information for vg0720170421:

Variant ID: vg0720170421 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 20170421
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.70, T: 0.29, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

CACGAATGAAAAAACTAATTTCAGAACTCGCCTGGAAACCGCGAGACGAATCTTTTGAGCCTACTTAAGCCGTCATTAGCACATGTGGGTTACTGTAGCA[T/C]
TTATGGCTAATCATGGCCTAATTAGGCTCAAAAGATTCGTCTCGCGATTTATAGCTAAACTGTGCAATTGGTTTTTCTTTTTGTCCACATTTAATGCTCC

Reverse complement sequence

GGAGCATTAAATGTGGACAAAAAGAAAAACCAATTGCACAGTTTAGCTATAAATCGCGAGACGAATCTTTTGAGCCTAATTAGGCCATGATTAGCCATAA[A/G]
TGCTACAGTAACCCACATGTGCTAATGACGGCTTAAGTAGGCTCAAAAGATTCGTCTCGCGGTTTCCAGGCGAGTTCTGAAATTAGTTTTTTCATTCGTG

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	26.30%	18.10%	0.66%	54.93%	NA
All Indica	2759	4.50%	11.10%	1.01%	83.40%	NA
All Japonica	1512	72.30%	11.40%	0.00%	16.34%	NA
Aus	269	0.00%	97.40%	0.00%	2.60%	NA
Indica I	595	2.20%	10.60%	1.51%	85.71%	NA
Indica II	465	4.70%	13.80%	0.65%	80.86%	NA
Indica III	913	6.70%	4.80%	0.22%	88.28%	NA
Indica Intermediate	786	3.40%	17.30%	1.78%	77.48%	NA
Temperate Japonica	767	96.50%	0.40%	0.00%	3.13%	NA
Tropical Japonica	504	34.50%	31.20%	0.00%	34.33%	NA
Japonica Intermediate	241	74.30%	5.00%	0.00%	20.75%	NA
VI/Aromatic	96	6.20%	92.70%	0.00%	1.04%	NA
Intermediate	90	24.40%	27.80%	3.33%	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
vg0720170421	T -> DEL	N	N	silent_mutation	Average:17.471; most accessible tissue: Callus, score: 54.251	N	N	N	N
vg0720170421	T -> C	LOC_Os07g33730.1	upstream_gene_variant ; 260.0bp to feature; MODIFIER	silent_mutation	Average:17.471; most accessible tissue: Callus, score: 54.251	N	N	N	N
vg0720170421	T -> C	LOC_Os07g33740.1	upstream_gene_variant ; 3539.0bp to feature; MODIFIER	silent_mutation	Average:17.471; most accessible tissue: Callus, score: 54.251	N	N	N	N
vg0720170421	T -> C	LOC_Os07g33730.2	upstream_gene_variant ; 260.0bp to feature; MODIFIER	silent_mutation	Average:17.471; most accessible tissue: Callus, score: 54.251	N	N	N	N
vg0720170421	T -> C	LOC_Os07g33730-LOC_Os07g33740	intergenic_region ; MODIFIER	silent_mutation	Average:17.471; most accessible tissue: Callus, score: 54.251	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0720170421	4.93E-06	4.93E-06	mr1110	Jap_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