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Detailed information for vg0720282120:

Variant ID: vg0720282120 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 20282120
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAATAAGAAATATTAGAAGTAGAGTATAGAGTCCATATAGGAATTTAAAACTAACTAAAATTCGGAAAAAAAAAGGAGCCTCTACGTTCGCTCCCATGGC[C/A]
TAGAAATTCTCACATTAATCGAAGAAAAAGAAAAAAACAGAGTTCATATAGAAATACAATTTAGAAATAGCTGAAATTCAGAATTAAAAATAAGGAATAT

Reverse complement sequence

ATATTCCTTATTTTTAATTCTGAATTTCAGCTATTTCTAAATTGTATTTCTATATGAACTCTGTTTTTTTCTTTTTCTTCGATTAATGTGAGAATTTCTA[G/T]
GCCATGGGAGCGAACGTAGAGGCTCCTTTTTTTTTCCGAATTTTAGTTAGTTTTAAATTCCTATATGGACTCTATACTCTACTTCTAATATTTCTTATTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.50%	10.40%	1.25%	10.90%	NA
All Indica	2759	74.10%	17.50%	1.52%	6.92%	NA
All Japonica	1512	79.00%	0.20%	0.46%	20.30%	NA
Aus	269	96.30%	0.00%	3.72%	0.00%	NA
Indica I	595	89.10%	2.00%	0.50%	8.40%	NA
Indica II	465	90.30%	7.10%	0.86%	1.72%	NA
Indica III	913	58.60%	34.40%	0.99%	6.02%	NA
Indica Intermediate	786	71.10%	15.60%	3.31%	9.92%	NA
Temperate Japonica	767	97.80%	0.10%	0.13%	1.96%	NA
Tropical Japonica	504	50.40%	0.40%	0.79%	48.41%	NA
Japonica Intermediate	241	79.30%	0.00%	0.83%	19.92%	NA
VI/Aromatic	96	93.80%	0.00%	0.00%	6.25%	NA
Intermediate	90	81.10%	6.70%	0.00%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0720282120	C -> DEL	N	N	silent_mutation	Average:16.433; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0720282120	C -> A	LOC_Os07g33910.2	upstream_gene_variant ; 2184.0bp to feature; MODIFIER	silent_mutation	Average:16.433; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0720282120	C -> A	LOC_Os07g33915.1	downstream_gene_variant ; 1197.0bp to feature; MODIFIER	silent_mutation	Average:16.433; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0720282120	C -> A	LOC_Os07g33915-LOC_Os07g33988	intergenic_region ; MODIFIER	silent_mutation	Average:16.433; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0720282120	NA	3.61E-06	mr1446_2	Ind_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
vg0720282120	NA	7.17E-06	mr1879_2	Ind_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