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Detailed information for vg0702286198:

Variant ID: vg0702286198 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 2286198
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.65, C: 0.35, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

TCCTCCGCGGCGGCGGCGTGCTTGACGCAGTATTCGATGACCTTGGCGAGGACCTTGGAGGCGACGTTGGGGAGAGGCACCCCGTTCGTCGTGCAGTCGT[T/C]
CTCGATCATGTTGGAGACGAGCTGCGACAGGCTCGCCGCCGCCGACGGCACGTTAAAGTGCTCGCCGTCGGAGCTGATTAAGAGGATCGTGTCGTCGGCA

Reverse complement sequence

TGCCGACGACACGATCCTCTTAATCAGCTCCGACGGCGAGCACTTTAACGTGCCGTCGGCGGCGGCGAGCCTGTCGCAGCTCGTCTCCAACATGATCGAG[A/G]
ACGACTGCACGACGAACGGGGTGCCTCTCCCCAACGTCGCCTCCAAGGTCCTCGCCAAGGTCATCGAATACTGCGTCAAGCACGCCGCCGCCGCGGAGGA

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	57.60%	42.10%	0.25%	0.00%	NA
All Indica	2759	86.20%	13.40%	0.33%	0.00%	NA
All Japonica	1512	0.90%	99.10%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	94.30%	5.40%	0.34%	0.00%	NA
Indica II	465	50.50%	48.80%	0.65%	0.00%	NA
Indica III	913	98.80%	1.10%	0.11%	0.00%	NA
Indica Intermediate	786	86.60%	13.00%	0.38%	0.00%	NA
Temperate Japonica	767	0.10%	99.90%	0.00%	0.00%	NA
Tropical Japonica	504	2.60%	97.40%	0.00%	0.00%	NA
Japonica Intermediate	241	0.00%	100.00%	0.00%	0.00%	NA
VI/Aromatic	96	28.10%	71.90%	0.00%	0.00%	NA
Intermediate	90	40.00%	56.70%	3.33%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0702286198	T -> C	LOC_Os07g05150.1	missense_variant ; p.Asn42Asp; MODERATE	nonsynonymous_codon	Average:44.795; most accessible tissue: Callus, score: 59.322	possibly damaging	-1.819	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0702286198	NA	7.07E-07	mr1004	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
vg0702286198	NA	5.82E-12	mr1005	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
vg0702286198	NA	1.72E-13	mr1874	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
vg0702286198	NA	1.12E-15	mr1950	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
vg0702286198	NA	2.40E-09	mr1158_2	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
vg0702286198	NA	2.79E-11	mr1383_2	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
vg0702286198	NA	1.87E-07	mr1654_2	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
vg0702286198	NA	1.47E-18	mr1874_2	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