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Detailed information for vg0706213471:

Variant ID: vg0706213471 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 6213471
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, T: 0.10, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

AGCTTTATGTTCTCGATGCTGCCCAACGGAGGTCCAGGGATGTTCAATAGCTGATCCATCATTAAAGTTGAGGAGATGTCGCCTCTGCATTGGATCTTGT[T/C]
GGCAAAGTACAGACCGATTGGCAATTGTCCCATTCCAAGTTGTCTGGCCGATGACATCGGATGATAAAACTCGTAAGAGACTTGGATATTTCTCCCTTGA

Reverse complement sequence

TCAAGGGAGAAATATCCAAGTCTCTTACGAGTTTTATCATCCGATGTCATCGGCCAGACAACTTGGAATGGGACAATTGCCAATCGGTCTGTACTTTGCC[A/G]
ACAAGATCCAATGCAGAGGCGACATCTCCTCAACTTTAATGATGGATCAGCTATTGAACATCCCTGGACCTCCGTTGGGCAGCATCGAGAACATAAAGCT

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	82.30%	14.80%	2.90%	0.00%	NA
All Indica	2759	78.80%	19.20%	1.92%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	10.80%	60.60%	28.62%	0.00%	NA
Indica I	595	77.10%	22.20%	0.67%	0.00%	NA
Indica II	465	99.10%	0.60%	0.22%	0.00%	NA
Indica III	913	72.60%	25.10%	2.30%	0.00%	NA
Indica Intermediate	786	75.30%	21.20%	3.44%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	88.90%	5.60%	5.56%	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
vg0706213471	T -> C	LOC_Os07g11270.1	missense_variant ; p.Asn407Asp; MODERATE	nonsynonymous_codon	Average:53.811; most accessible tissue: Minghui63 flag leaf, score: 77.828	benign	-0.777	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0706213471	NA	1.29E-09	mr1063	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
vg0706213471	NA	7.10E-06	mr1170	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
vg0706213471	NA	7.13E-06	mr1177	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
vg0706213471	NA	5.23E-11	mr1180	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
vg0706213471	NA	1.08E-07	mr1213	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
vg0706213471	NA	7.69E-07	mr1220	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
vg0706213471	NA	9.30E-08	mr1343	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
vg0706213471	NA	1.97E-07	mr1352	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
vg0706213471	NA	9.79E-07	mr1422	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
vg0706213471	7.89E-07	1.57E-10	mr1806	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
vg0706213471	NA	7.61E-07	mr1063_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
vg0706213471	NA	5.64E-09	mr1378_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
vg0706213471	NA	4.13E-08	mr1870_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