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Detailed information for vg0812027729:

Variant ID: vg0812027729 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 12027729
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTGTGGTGACATGCTGATGGGCGTCTTATAAGCAGTCCTATATGCCCAAAATGCATCAGGTAGCTTGTTCTTCCATGTCTTCCCCATCTCATTGACAGT[T/C]
TTCTACAGAATGTTCTTGATTTGTTTGTTGCTCGTTTCTGCTTGTCCACTTGTCTGGGGATGATACGGAGTGGCAATGTTGTGCTGAGCTCCGAGCTCTT

Reverse complement sequence

AAGAGCTCGGAGCTCAGCACAACATTGCCACTCCGTATCATCCCCAGACAAGTGGACAAGCAGAAACGAGCAACAAACAAATCAAGAACATTCTGTAGAA[A/G]
ACTGTCAATGAGATGGGGAAGACATGGAAGAACAAGCTACCTGATGCATTTTGGGCATATAGGACTGCTTATAAGACGCCCATCAGCATGTCACCACACC

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	89.70%	2.00%	3.47%	4.89%	NA
All Indica	2759	92.30%	1.40%	3.81%	2.46%	NA
All Japonica	1512	91.80%	3.20%	1.98%	2.98%	NA
Aus	269	46.80%	0.70%	9.67%	42.75%	NA
Indica I	595	96.30%	0.00%	2.69%	1.01%	NA
Indica II	465	96.10%	0.60%	2.37%	0.86%	NA
Indica III	913	88.90%	3.50%	4.60%	2.96%	NA
Indica Intermediate	786	90.80%	0.60%	4.58%	3.94%	NA
Temperate Japonica	767	96.90%	0.40%	1.04%	1.69%	NA
Tropical Japonica	504	84.70%	8.50%	4.17%	2.58%	NA
Japonica Intermediate	241	90.50%	1.20%	0.41%	7.88%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	2.20%	3.33%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0812027729	T -> C	LOC_Os08g20060.1	downstream_gene_variant ; 3.0bp to feature; MODIFIER	silent_mutation	Average:11.896; most accessible tissue: Callus, score: 34.341	N	N	N	N
vg0812027729	T -> C	LOC_Os08g20050-LOC_Os08g20060	intergenic_region ; MODIFIER	silent_mutation	Average:11.896; most accessible tissue: Callus, score: 34.341	N	N	N	N
vg0812027729	T -> DEL	N	N	silent_mutation	Average:11.896; most accessible tissue: Callus, score: 34.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0812027729	9.24E-06	5.72E-08	mr1073	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
vg0812027729	NA	2.77E-06	mr1583	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