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Detailed information for vg0521975971:

Variant ID: vg0521975971 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 21975971
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCACTTTAAAGCAGTATATACTACATAGAAATGTTCAGTATGTGTCACATGAGAAAGTTCAGTATATGCTATCTTCTAGGAAAGTTCAGTATGTATCACA[T/C]
AGAAAAGTTCAGTGTGTGCTATATTGCAGAGGAGTTCAGTATGTTGCACAGAAAATTCAGAACATACTATATGCTGTCGTATAACAAAGTTCAGTACATA

Reverse complement sequence

TATGTACTGAACTTTGTTATACGACAGCATATAGTATGTTCTGAATTTTCTGTGCAACATACTGAACTCCTCTGCAATATAGCACACACTGAACTTTTCT[A/G]
TGTGATACATACTGAACTTTCCTAGAAGATAGCATATACTGAACTTTCTCATGTGACACATACTGAACATTTCTATGTAGTATATACTGCTTTAAAGTGA

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	39.40%	0.10%	9.25%	51.25%	NA
All Indica	2759	4.00%	0.20%	14.39%	81.41%	NA
All Japonica	1512	98.70%	0.00%	0.20%	1.12%	NA
Aus	269	45.00%	0.00%	11.15%	43.87%	NA
Indica I	595	2.00%	0.70%	18.15%	79.16%	NA
Indica II	465	5.60%	0.20%	8.60%	85.59%	NA
Indica III	913	2.30%	0.00%	17.74%	79.96%	NA
Indica Intermediate	786	6.60%	0.00%	11.07%	82.32%	NA
Temperate Japonica	767	98.70%	0.00%	0.13%	1.17%	NA
Tropical Japonica	504	99.20%	0.00%	0.00%	0.79%	NA
Japonica Intermediate	241	97.50%	0.00%	0.83%	1.66%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	48.90%	0.00%	7.78%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0521975971	T -> DEL	N	N	silent_mutation	Average:10.26; most accessible tissue: Callus, score: 24.036	N	N	N	N
vg0521975971	T -> C	LOC_Os05g37530.1	downstream_gene_variant ; 4788.0bp to feature; MODIFIER	silent_mutation	Average:10.26; most accessible tissue: Callus, score: 24.036	N	N	N	N
vg0521975971	T -> C	LOC_Os05g37550.1	downstream_gene_variant ; 4116.0bp to feature; MODIFIER	silent_mutation	Average:10.26; most accessible tissue: Callus, score: 24.036	N	N	N	N
vg0521975971	T -> C	LOC_Os05g37540.1	intron_variant ; MODIFIER	silent_mutation	Average:10.26; most accessible tissue: Callus, score: 24.036	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0521975971	1.28E-07	NA	mr1191_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
vg0521975971	1.55E-06	1.21E-07	mr1191_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