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Detailed information for vg1209962192:

Variant ID: vg1209962192 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 9962192
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.69, T: 0.31, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

GGCACCACAAAGGATGGAGTGAAGCTCACTAGCTCTCAACTCCTTACTCTCTCAATCCAACTCTCTCCCCTTCTCAAATCCCCCTCACAAAGAGGCACCA[T/C]
AAAGGTAGGGAAATGGGGATGGCTATTTGGCTTTGGATGTGTCTAATACTCCCCAAGAGCAGCAGCCACTCAAAGGAGGGGTGGAGGAGTTTATATACCC

Reverse complement sequence

GGGTATATAAACTCCTCCACCCCTCCTTTGAGTGGCTGCTGCTCTTGGGGAGTATTAGACACATCCAAAGCCAAATAGCCATCCCCATTTCCCTACCTTT[A/G]
TGGTGCCTCTTTGTGAGGGGGATTTGAGAAGGGGAGAGAGTTGGATTGAGAGAGTAAGGAGTTGAGAGCTAGTGAGCTTCACTCCATCCTTTGTGGTGCC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	32.60%	10.90%	19.34%	37.18%	NA
All Indica	2759	11.30%	18.10%	31.46%	39.11%	NA
All Japonica	1512	76.80%	0.10%	0.86%	22.29%	NA
Aus	269	4.80%	1.10%	2.60%	91.45%	NA
Indica I	595	16.60%	16.10%	31.09%	36.13%	NA
Indica II	465	16.60%	15.10%	17.63%	50.75%	NA
Indica III	913	5.60%	21.80%	43.26%	29.35%	NA
Indica Intermediate	786	10.90%	17.00%	26.21%	45.80%	NA
Temperate Japonica	767	85.10%	0.10%	0.52%	14.21%	NA
Tropical Japonica	504	68.10%	0.00%	1.39%	30.56%	NA
Japonica Intermediate	241	68.50%	0.00%	0.83%	30.71%	NA
VI/Aromatic	96	11.50%	7.30%	11.46%	69.79%	NA
Intermediate	90	45.60%	6.70%	16.67%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1209962192	T -> C	LOC_Os12g17390.1	upstream_gene_variant ; 976.0bp to feature; MODIFIER	silent_mutation	Average:30.618; most accessible tissue: Minghui63 flag leaf, score: 68.675	N	N	N	N
vg1209962192	T -> C	LOC_Os12g17390-LOC_Os12g17400	intergenic_region ; MODIFIER	silent_mutation	Average:30.618; most accessible tissue: Minghui63 flag leaf, score: 68.675	N	N	N	N
vg1209962192	T -> DEL	N	N	silent_mutation	Average:30.618; most accessible tissue: Minghui63 flag leaf, score: 68.675	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209962192	NA	1.12E-08	mr1301	Ind_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
vg1209962192	NA	6.73E-09	mr1546	Ind_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
vg1209962192	2.22E-06	7.28E-07	mr1825	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