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Detailed information for vg0702562003:

Variant ID: vg0702562003 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 2562003
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATATATAGAAATTTTATTCTCATAGTTTAAAATATGATGAAAATTACTTAAAAAATAGAAAACAAACTAAATTGAAAATTAAGAGAAGTACAACATTAA[T/G]
ATTAGTTTAGAACTTCAAAAATTGTTAATAAGAATTGCTTGTCGAAAGAGTTTTTAATTATTTTATCATTACTGTTTGACTGTCATTATTGTACGAAAAT

Reverse complement sequence

ATTTTCGTACAATAATGACAGTCAAACAGTAATGATAAAATAATTAAAAACTCTTTCGACAAGCAATTCTTATTAACAATTTTTGAAGTTCTAAACTAAT[A/C]
TTAATGTTGTACTTCTCTTAATTTTCAATTTAGTTTGTTTTCTATTTTTTAAGTAATTTTCATCATATTTTAAACTATGAGAATAAAATTTCTATATATT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.50%	1.40%	2.12%	0.00%	NA
All Indica	2759	95.60%	1.60%	2.83%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	87.40%	6.30%	6.32%	0.00%	NA
Indica I	595	97.80%	0.00%	2.18%	0.00%	NA
Indica II	465	96.60%	1.50%	1.94%	0.00%	NA
Indica III	913	93.60%	2.80%	3.50%	0.00%	NA
Indica Intermediate	786	95.50%	1.40%	3.05%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	90.60%	5.20%	4.17%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg0702562003	T -> G	LOC_Os07g05500.1	upstream_gene_variant ; 3437.0bp to feature; MODIFIER	silent_mutation	Average:24.59; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0702562003	T -> G	LOC_Os07g05490.1	intron_variant ; MODIFIER	silent_mutation	Average:24.59; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0702562003	4.16E-06	NA	mr1889	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