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Detailed information for vg0202989689:

Variant ID: vg0202989689 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2989689
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

TGTCGTCTGCACGACAGGTGAGCACTCGGAGAATCGAGCGCATCGACTCCACCATCCGCGTGTACGTCGTCAGGTGCTCCTCTACGGGTACCGGAATCCC[T/C]
GCGTCTAAACGTTGGATCGTCGTTGAACCGTCAACGACGACCCGGTTGATGTCGTCGACCTGCATGGTTAATTTGTTCATACATATTCGTAACATTTGAC

Reverse complement sequence

GTCAAATGTTACGAATATGTATGAACAAATTAACCATGCAGGTCGACGACATCAACCGGGTCGTCGTTGACGGTTCAACGACGATCCAACGTTTAGACGC[A/G]
GGGATTCCGGTACCCGTAGAGGAGCACCTGACGACGTACACGCGGATGGTGGAGTCGATGCGCTCGATTCTCCGAGTGCTCACCTGTCGTGCAGACGACA

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	78.80%	20.30%	0.80%	0.11%	NA
All Indica	2759	97.40%	2.40%	0.25%	0.00%	NA
All Japonica	1512	39.90%	57.90%	1.92%	0.33%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	95.80%	3.40%	0.84%	0.00%	NA
Indica II	465	98.30%	1.50%	0.22%	0.00%	NA
Indica III	913	97.20%	2.70%	0.11%	0.00%	NA
Indica Intermediate	786	98.30%	1.70%	0.00%	0.00%	NA
Temperate Japonica	767	15.50%	83.10%	1.30%	0.13%	NA
Tropical Japonica	504	83.70%	12.30%	3.17%	0.79%	NA
Japonica Intermediate	241	25.70%	73.00%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	76.70%	21.10%	2.22%	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
vg0202989689	T -> DEL	LOC_Os02g05990.1	N	frameshift_variant	Average:28.043; most accessible tissue: Zhenshan97 flag leaf, score: 43.728	N	N	N	N
vg0202989689	T -> C	LOC_Os02g05990.1	synonymous_variant ; p.Ala432Ala; LOW	synonymous_codon	Average:28.043; most accessible tissue: Zhenshan97 flag leaf, score: 43.728	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0202989689	NA	1.53E-06	mr1029	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
vg0202989689	NA	9.63E-06	mr1725	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
vg0202989689	NA	1.18E-07	mr1308_2	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
vg0202989689	NA	5.78E-09	mr1361_2	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
vg0202989689	NA	7.10E-12	mr1368_2	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
vg0202989689	NA	7.86E-07	mr1379_2	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
vg0202989689	NA	1.81E-08	mr1401_2	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
vg0202989689	NA	2.81E-10	mr1584_2	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
vg0202989689	NA	1.37E-07	mr1606_2	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
vg0202989689	NA	4.33E-06	mr1633_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
vg0202989689	NA	5.53E-06	mr1633_2	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
vg0202989689	NA	2.16E-17	mr1682_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
vg0202989689	3.65E-06	2.25E-07	mr1683_2	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
vg0202989689	7.83E-06	3.10E-06	mr1687_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