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Detailed information for vg1207623185:

Variant ID: vg1207623185 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 7623185
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, T: 0.02, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

TCTGGAGCTGGAGCTCAGCCAAACAGTTTCGGCTCCACCAAAACTGGGAGTGGAGCTGGGTGGAGCTCTCTCACAAAATGAACTAGAGTTGTGGAGCTGG[G/T]
TTTAGGCAGCTCCACAACTCCACTCCAGACTCAACTCTTGGAGTTAAATTTAGGAGTTGGAGCTATACCAAACAGGCCCTATGTTTTGCAATGGACACGA

Reverse complement sequence

TCGTGTCCATTGCAAAACATAGGGCCTGTTTGGTATAGCTCCAACTCCTAAATTTAACTCCAAGAGTTGAGTCTGGAGTGGAGTTGTGGAGCTGCCTAAA[C/A]
CCAGCTCCACAACTCTAGTTCATTTTGTGAGAGAGCTCCACCCAGCTCCACTCCCAGTTTTGGTGGAGCCGAAACTGTTTGGCTGAGCTCCAGCTCCAGA

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	58.60%	41.00%	0.30%	0.11%	NA
All Indica	2759	33.00%	66.30%	0.47%	0.18%	NA
All Japonica	1512	95.00%	5.00%	0.00%	0.00%	NA
Aus	269	97.40%	2.60%	0.00%	0.00%	NA
Indica I	595	49.20%	49.60%	1.01%	0.17%	NA
Indica II	465	13.10%	86.70%	0.22%	0.00%	NA
Indica III	913	27.50%	72.00%	0.22%	0.33%	NA
Indica Intermediate	786	38.90%	60.40%	0.51%	0.13%	NA
Temperate Japonica	767	94.40%	5.60%	0.00%	0.00%	NA
Tropical Japonica	504	94.20%	5.80%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	75.60%	23.30%	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
vg1207623185	G -> DEL	N	N	silent_mutation	Average:53.386; most accessible tissue: Minghui63 root, score: 65.279	N	N	N	N
vg1207623185	G -> T	LOC_Os12g13570.1	upstream_gene_variant ; 3106.0bp to feature; MODIFIER	silent_mutation	Average:53.386; most accessible tissue: Minghui63 root, score: 65.279	N	N	N	N
vg1207623185	G -> T	LOC_Os12g13580.1	intron_variant ; MODIFIER	silent_mutation	Average:53.386; most accessible tissue: Minghui63 root, score: 65.279	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207623185	NA	1.61E-16	Plant_height	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1207623185	NA	6.09E-09	mr1002_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