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Detailed information for vg1213799974:

Variant ID: vg1213799974 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13799974
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTAAAATTCAATAGTTGTATCCCGTGCAACGCACGGGTTGACGGCTAGTACAACTTTGCCCCATAACCATTTTTTCCTTGGTTATACAAAAAAACGATAT[G/T]
CATATCCATGTAGTGGCTTCTAGAGATGGAAACGTTGTTCGGAAAGTTTTCGTCTTCTAGGTGTGTTTTTTGAAATGGAAAGTGTTCGACGAAATTATTC

Reverse complement sequence

GAATAATTTCGTCGAACACTTTCCATTTCAAAAAACACACCTAGAAGACGAAAACTTTCCGAACAACGTTTCCATCTCTAGAAGCCACTACATGGATATG[C/A]
ATATCGTTTTTTTGTATAACCAAGGAAAAAATGGTTATGGGGCAAAGTTGTACTAGCCGTCAACCCGTGCGTTGCACGGGATACAACTATTGAATTTTAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.40%	14.50%	0.13%	0.00%	NA
All Indica	2759	82.70%	17.10%	0.14%	0.00%	NA
All Japonica	1512	87.80%	12.10%	0.07%	0.00%	NA
Aus	269	97.40%	2.60%	0.00%	0.00%	NA
Indica I	595	77.10%	22.40%	0.50%	0.00%	NA
Indica II	465	95.70%	4.30%	0.00%	0.00%	NA
Indica III	913	82.00%	18.00%	0.00%	0.00%	NA
Indica Intermediate	786	80.20%	19.70%	0.13%	0.00%	NA
Temperate Japonica	767	95.60%	4.30%	0.13%	0.00%	NA
Tropical Japonica	504	85.70%	14.30%	0.00%	0.00%	NA
Japonica Intermediate	241	67.60%	32.40%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	77.80%	21.10%	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
vg1213799974	G -> T	LOC_Os12g24210.1	upstream_gene_variant ; 1100.0bp to feature; MODIFIER	silent_mutation	Average:45.977; most accessible tissue: Minghui63 root, score: 63.193	N	N	N	N
vg1213799974	G -> T	LOC_Os12g24220.1	downstream_gene_variant ; 2232.0bp to feature; MODIFIER	silent_mutation	Average:45.977; most accessible tissue: Minghui63 root, score: 63.193	N	N	N	N
vg1213799974	G -> T	LOC_Os12g24210-LOC_Os12g24220	intergenic_region ; MODIFIER	silent_mutation	Average:45.977; most accessible tissue: Minghui63 root, score: 63.193	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213799974	2.37E-06	NA	mr1291_2	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