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Detailed information for vg0600352193:

Variant ID: vg0600352193 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 352193
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

AAGAATAAGGAAGAATAAAGAAAAATAATTCGAAGGGTAGAACCGTACTTACACAGCTGTTTCTCTCTCCTATTCCTCTAAAAATAATAAAATAATGACA[C/T]
GGGTGTCCAGGAGCTAATGTCCAGTTTTTTGCGATGTTCTATAGCAAATACGCGTTTTTGCGGTGTCCCATAGCTAATTATACGTTTTTTGGGTGTCCTG

Reverse complement sequence

CAGGACACCCAAAAAACGTATAATTAGCTATGGGACACCGCAAAAACGCGTATTTGCTATAGAACATCGCAAAAAACTGGACATTAGCTCCTGGACACCC[G/A]
TGTCATTATTTTATTATTTTTAGAGGAATAGGAGAGAGAAACAGCTGTGTAAGTACGGTTCTACCCTTCGAATTATTTTTCTTTATTCTTCCTTATTCTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.40%	33.80%	0.36%	23.44%	NA
All Indica	2759	14.00%	47.70%	0.54%	37.73%	NA
All Japonica	1512	96.00%	0.50%	0.07%	3.44%	NA
Aus	269	32.00%	66.90%	0.00%	1.12%	NA
Indica I	595	2.00%	58.70%	0.67%	38.66%	NA
Indica II	465	37.60%	44.70%	0.86%	16.77%	NA
Indica III	913	7.00%	40.70%	0.22%	52.03%	NA
Indica Intermediate	786	17.20%	49.40%	0.64%	32.82%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	89.50%	0.40%	0.20%	9.92%	NA
Japonica Intermediate	241	97.10%	2.10%	0.00%	0.83%	NA
VI/Aromatic	96	24.00%	76.00%	0.00%	0.00%	NA
Intermediate	90	62.20%	23.30%	1.11%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0600352193	C -> T	LOC_Os06g01590.1	upstream_gene_variant ; 3677.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0600352193	C -> T	LOC_Os06g01600.1	upstream_gene_variant ; 217.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0600352193	C -> T	LOC_Os06g01600-LOC_Os06g01610	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0600352193	C -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0600352193	NA	7.47E-06	mr1195	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
vg0600352193	NA	1.25E-07	mr1252	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
vg0600352193	NA	1.23E-06	mr1436	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
vg0600352193	NA	1.69E-06	mr1496	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
vg0600352193	NA	6.02E-06	mr1525	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
vg0600352193	NA	5.07E-06	mr1679	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
vg0600352193	NA	4.92E-06	mr1807	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