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Detailed information for vg1205876728:

Variant ID: vg1205876728 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 5876728
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAACACTCTCTACGTTCTTTATACGCTTGGCTCCCTTTTCATCAAAGGATTTGTTATAAGGAACAATTCTATAGGATTTTTTTTCTATTTTTTTGCCCTT[T/C]
CAACAAATGATTGATGACTTCAAAATCCTGTGAAATTCTTTTGGAGTGGATTAGATTAATACATGTTTTTTTTCAAAAAAAGTTAGCATGCATGGGGTCT

Reverse complement sequence

AGACCCCATGCATGCTAACTTTTTTTGAAAAAAAACATGTATTAATCTAATCCACTCCAAAAGAATTTCACAGGATTTTGAAGTCATCAATCATTTGTTG[A/G]
AAGGGCAAAAAAATAGAAAAAAAATCCTATAGAATTGTTCCTTATAACAAATCCTTTGATGAAAAGGGAGCCAAGCGTATAAAGAACGTAGAGAGTGTTC

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	61.30%	8.60%	0.91%	29.24%	NA
All Indica	2759	74.80%	9.70%	0.43%	15.11%	NA
All Japonica	1512	38.20%	2.80%	1.79%	57.14%	NA
Aus	269	70.30%	0.70%	1.49%	27.51%	NA
Indica I	595	45.90%	13.30%	0.84%	40.00%	NA
Indica II	465	94.40%	3.20%	0.43%	1.94%	NA
Indica III	913	86.30%	9.90%	0.00%	3.83%	NA
Indica Intermediate	786	71.60%	10.60%	0.64%	17.18%	NA
Temperate Japonica	767	49.40%	4.80%	2.22%	43.55%	NA
Tropical Japonica	504	19.40%	0.40%	1.39%	78.77%	NA
Japonica Intermediate	241	41.90%	1.70%	1.24%	55.19%	NA
VI/Aromatic	96	13.50%	84.40%	0.00%	2.08%	NA
Intermediate	90	57.80%	14.40%	0.00%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1205876728	T -> C	LOC_Os12g10890.1	downstream_gene_variant ; 4054.0bp to feature; MODIFIER	silent_mutation	Average:46.72; most accessible tissue: Callus, score: 87.007	N	N	N	N
vg1205876728	T -> C	LOC_Os12g10880-LOC_Os12g10890	intergenic_region ; MODIFIER	silent_mutation	Average:46.72; most accessible tissue: Callus, score: 87.007	N	N	N	N
vg1205876728	T -> DEL	N	N	silent_mutation	Average:46.72; most accessible tissue: Callus, score: 87.007	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1205876728	1.50E-06	2.65E-11	mr1585_2	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