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Detailed information for vg1215369377:

Variant ID: vg1215369377 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15369377
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCATGAATAAAAATCCAAATTGCACTCCCATGACTACGCATGGTACTTGTATAATGTAAACAAAAAACTTCCGGAAGAATGAAACATGAATAACGTCGT[T/G]
AACTTGAACATGAAGTGAAATATGAATATGTAGCATAATACCAAAACCACACAATTAATAATAGGAAGCTTCGAATAATAATTGGGTAAATGAAACCAAC

Reverse complement sequence

GTTGGTTTCATTTACCCAATTATTATTCGAAGCTTCCTATTATTAATTGTGTGGTTTTGGTATTATGCTACATATTCATATTTCACTTCATGTTCAAGTT[A/C]
ACGACGTTATTCATGTTTCATTCTTCCGGAAGTTTTTTGTTTACATTATACAAGTACCATGCGTAGTCATGGGAGTGCAATTTGGATTTTTATTCATGAT

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	25.80%	0.70%	1.35%	72.11%	NA
All Indica	2759	4.40%	1.20%	2.07%	92.39%	NA
All Japonica	1512	67.90%	0.00%	0.20%	31.88%	NA
Aus	269	8.20%	0.40%	1.12%	90.33%	NA
Indica I	595	4.50%	0.50%	1.18%	93.78%	NA
Indica II	465	4.90%	1.10%	2.80%	91.18%	NA
Indica III	913	1.80%	1.80%	1.53%	94.96%	NA
Indica Intermediate	786	7.00%	1.00%	2.93%	89.06%	NA
Temperate Japonica	767	91.40%	0.00%	0.00%	8.60%	NA
Tropical Japonica	504	35.10%	0.00%	0.40%	64.48%	NA
Japonica Intermediate	241	61.80%	0.00%	0.41%	37.76%	NA
VI/Aromatic	96	11.50%	0.00%	0.00%	88.54%	NA
Intermediate	90	44.40%	0.00%	1.11%	54.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215369377	T -> DEL	N	N	silent_mutation	Average:11.494; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg1215369377	T -> G	LOC_Os12g26320.1	upstream_gene_variant ; 1188.0bp to feature; MODIFIER	silent_mutation	Average:11.494; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg1215369377	T -> G	LOC_Os12g26320-LOC_Os12g26330	intergenic_region ; MODIFIER	silent_mutation	Average:11.494; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215369377	3.11E-06	NA	mr1553	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