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Detailed information for vg0508574937:

Variant ID: vg0508574937 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 8574937
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCACGTAGAATTGACTCGTTGAGTCGGTATCTCGTGAGGTTCGCTTGCAAGATTAATCTTAGCCGTCCAAAATTGATATAAATCCGTTCTTTCTTTTCAA[T/A]
GACATATTATTCCTTTTTAATATATGTCATCTACCAAATATGATCTAATCTTTTTCCGGAGGATGTTTTAATCTTCTGTCTCAGCTATAAATCATTTGTA

Reverse complement sequence

TACAAATGATTTATAGCTGAGACAGAAGATTAAAACATCCTCCGGAAAAAGATTAGATCATATTTGGTAGATGACATATATTAAAAAGGAATAATATGTC[A/T]
TTGAAAAGAAAGAACGGATTTATATCAATTTTGGACGGCTAAGATTAATCTTGCAAGCGAACCTCACGAGATACCGACTCAACGAGTCAATTCTACGTGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.50%	3.70%	0.06%	4.78%	NA
All Indica	2759	86.50%	6.30%	0.07%	7.14%	NA
All Japonica	1512	98.10%	0.00%	0.00%	1.92%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.00%	0.30%	0.00%	0.67%	NA
Indica II	465	71.40%	12.50%	0.22%	15.91%	NA
Indica III	913	84.40%	9.60%	0.11%	5.81%	NA
Indica Intermediate	786	88.30%	3.30%	0.00%	8.40%	NA
Temperate Japonica	767	96.30%	0.00%	0.00%	3.65%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	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
vg0508574937	T -> DEL	N	N	silent_mutation	Average:48.122; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg0508574937	T -> A	LOC_Os05g15100.1	upstream_gene_variant ; 2835.0bp to feature; MODIFIER	silent_mutation	Average:48.122; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg0508574937	T -> A	LOC_Os05g15090.1	downstream_gene_variant ; 4854.0bp to feature; MODIFIER	silent_mutation	Average:48.122; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg0508574937	T -> A	LOC_Os05g15110.1	intron_variant ; MODIFIER	silent_mutation	Average:48.122; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0508574937	2.71E-06	NA	mr1902_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