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Detailed information for vg0206348169:

Variant ID: vg0206348169 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 6348169
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTCCATATTTTTCGGTTATCACCGTTCGTCTTCCTTAAGTTGGTTTGAACTTTGATATCTGGTATATAAAAACTTTACTTTTGTTTCTCGCGTGACGG[T/C]
TGTATTTTCATAATTGAGTTTCAACTTGGTACTTTTAGTTGGATTTCTTCAATCATAAAGTTTTATCTTTTCCCAACTTCTCTTTGGACTTCAAAGCTTT

Reverse complement sequence

AAAGCTTTGAAGTCCAAAGAGAAGTTGGGAAAAGATAAAACTTTATGATTGAAGAAATCCAACTAAAAGTACCAAGTTGAAACTCAATTATGAAAATACA[A/G]
CCGTCACGCGAGAAACAAAAGTAAAGTTTTTATATACCAGATATCAAAGTTCAAACCAACTTAAGGAAGACGAACGGTGATAACCGAAAAATATGGAAAC

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	37.50%	0.70%	4.15%	57.68%	NA
All Indica	2759	5.40%	0.40%	2.75%	91.41%	NA
All Japonica	1512	96.60%	0.10%	0.26%	3.04%	NA
Aus	269	21.20%	5.90%	34.94%	37.92%	NA
Indica I	595	5.50%	0.00%	0.34%	94.12%	NA
Indica II	465	9.70%	0.60%	1.94%	87.74%	NA
Indica III	913	2.80%	0.10%	3.29%	93.76%	NA
Indica Intermediate	786	5.70%	1.00%	4.45%	88.80%	NA
Temperate Japonica	767	97.40%	0.00%	0.00%	2.61%	NA
Tropical Japonica	504	96.00%	0.00%	0.40%	3.57%	NA
Japonica Intermediate	241	95.00%	0.80%	0.83%	3.32%	NA
VI/Aromatic	96	62.50%	4.20%	16.67%	16.67%	NA
Intermediate	90	48.90%	0.00%	6.67%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0206348169	T -> DEL	N	N	silent_mutation	Average:7.928; most accessible tissue: Callus, score: 21.662	N	N	N	N
vg0206348169	T -> C	LOC_Os02g12210.1	upstream_gene_variant ; 942.0bp to feature; MODIFIER	silent_mutation	Average:7.928; most accessible tissue: Callus, score: 21.662	N	N	N	N
vg0206348169	T -> C	LOC_Os02g12200.1	downstream_gene_variant ; 3759.0bp to feature; MODIFIER	silent_mutation	Average:7.928; most accessible tissue: Callus, score: 21.662	N	N	N	N
vg0206348169	T -> C	LOC_Os02g12210-LOC_Os02g12220	intergenic_region ; MODIFIER	silent_mutation	Average:7.928; most accessible tissue: Callus, score: 21.662	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0206348169	4.62E-06	2.94E-07	mr1930	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