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Detailed information for vg1205449240:

Variant ID: vg1205449240 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 5449240
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCTGGGTAAAATTCACTATCGGCCTGTTTGGTTGGAGGAAGTTTTTAGAAGGGATTGGGAATTTAAAGGGATGAGGCTATTAAGTGTTTTGTTTGGTTG[G/T]
GAGACATGGGAATTTTGGTGGGATGGGGATGGGGAATTGAGGAAGAAACTCCCTCCTTTTCAATACCTGAGTAGGGGCGGGTAATTGGGAGGGAATTTCT

Reverse complement sequence

AGAAATTCCCTCCCAATTACCCGCCCCTACTCAGGTATTGAAAAGGAGGGAGTTTCTTCCTCAATTCCCCATCCCCATCCCACCAAAATTCCCATGTCTC[C/A]
CAACCAAACAAAACACTTAATAGCCTCATCCCTTTAAATTCCCAATCCCTTCTAAAAACTTCCTCCAACCAAACAGGCCGATAGTGAATTTTACCCAGCT

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	33.50%	2.60%	3.03%	60.88%	NA
All Indica	2759	4.20%	0.00%	2.17%	93.58%	NA
All Japonica	1512	83.70%	7.90%	1.32%	7.01%	NA
Aus	269	20.10%	0.00%	20.82%	59.11%	NA
Indica I	595	2.70%	0.00%	2.18%	95.13%	NA
Indica II	465	4.30%	0.20%	0.65%	94.84%	NA
Indica III	913	2.70%	0.00%	3.07%	94.19%	NA
Indica Intermediate	786	7.00%	0.00%	2.04%	90.97%	NA
Temperate Japonica	767	91.10%	0.50%	0.78%	7.56%	NA
Tropical Japonica	504	73.60%	20.60%	1.59%	4.17%	NA
Japonica Intermediate	241	81.30%	5.00%	2.49%	11.20%	NA
VI/Aromatic	96	92.70%	0.00%	3.12%	4.17%	NA
Intermediate	90	63.30%	3.30%	4.44%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1205449240	G -> DEL	N	N	silent_mutation	Average:19.069; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg1205449240	G -> T	LOC_Os12g10310.1	downstream_gene_variant ; 1441.0bp to feature; MODIFIER	silent_mutation	Average:19.069; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg1205449240	G -> T	LOC_Os12g10310-LOC_Os12g10320	intergenic_region ; MODIFIER	silent_mutation	Average:19.069; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1205449240	2.09E-06	2.09E-06	mr1261	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
vg1205449240	9.45E-06	NA	mr1150_2	Jap_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