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Detailed information for vg0317064370:

Variant ID: vg0317064370 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 17064370
Reference Allele: A	Alternative Allele: G,C
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.08, others allele: 0.00, population size: 182. )

Flanking Sequence (100 bp) in Reference Genome:

GTTTGCTAACCTTGAAAAGTGCATCTTTTGCACGGAACGAGTTTCATTTCTTGGATATATTGTTACTCCACAGGGAATTGAGGTGGATGAGATGAAAATT[A/G,C]
AAGCCATAAAGAGTTGGCCGGTTCCCCAAACCATCACACAGGTGAGGAGTTTTCTTGGTCTTGCAGGATTCTATCATCGTTTCGTCAAAGATTTTAGTAC

Reverse complement sequence

GTACTAAAATCTTTGACGAAACGATGATAGAATCCTGCAAGACCAAGAAAACTCCTCACCTGTGTGATGGTTTGGGGAACCGGCCAACTCTTTATGGCTT[T/C,G]
AATTTTCATCTCATCCACCTCAATTCCCTGTGGAGTAACAATATATCCAAGAAATGAAACTCGTTCCGTGCAAAAGATGCACTTTTCAAGGTTAGCAAAC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.10%	28.10%	4.93%	5.82%	C: 0.02%
All Indica	2759	88.50%	7.40%	1.52%	2.57%	C: 0.04%
All Japonica	1512	4.10%	70.60%	11.97%	13.36%	NA
Aus	269	94.40%	5.20%	0.37%	0.00%	NA
Indica I	595	97.80%	1.70%	0.50%	0.00%	NA
Indica II	465	85.80%	6.50%	3.01%	4.73%	NA
Indica III	913	80.90%	13.30%	1.31%	4.38%	C: 0.11%
Indica Intermediate	786	91.70%	5.50%	1.65%	1.15%	NA
Temperate Japonica	767	0.30%	66.90%	15.38%	17.47%	NA
Tropical Japonica	504	11.30%	77.20%	6.35%	5.16%	NA
Japonica Intermediate	241	1.20%	68.50%	12.86%	17.43%	NA
VI/Aromatic	96	83.30%	15.60%	1.04%	0.00%	NA
Intermediate	90	57.80%	31.10%	8.89%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0317064370	A -> C	LOC_Os03g29940.1	missense_variant ; p.Lys733Gln; MODERATE	nonsynonymous_codon ; K733Q	Average:30.314; most accessible tissue: Minghui63 flag leaf, score: 53.617	benign	0.968	TOLERATED	0.08
vg0317064370	A -> DEL	LOC_Os03g29940.1	N	frameshift_variant	Average:30.314; most accessible tissue: Minghui63 flag leaf, score: 53.617	N	N	N	N
vg0317064370	A -> G	LOC_Os03g29940.1	missense_variant ; p.Lys733Glu; MODERATE	nonsynonymous_codon ; K733E	Average:30.314; most accessible tissue: Minghui63 flag leaf, score: 53.617	benign	0.498	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0317064370	1.10E-06	NA	mr1038_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
vg0317064370	2.04E-06	NA	mr1038_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
vg0317064370	1.21E-06	NA	mr1141_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
vg0317064370	7.01E-06	NA	mr1141_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
vg0317064370	NA	2.98E-09	mr1299_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
vg0317064370	NA	9.27E-07	mr1358_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
vg0317064370	NA	8.82E-12	mr1377_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
vg0317064370	8.96E-06	NA	mr1389_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
vg0317064370	NA	6.72E-06	mr1391_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
vg0317064370	NA	9.92E-18	mr1416_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
vg0317064370	NA	3.85E-25	mr1484_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
vg0317064370	NA	5.11E-19	mr1637_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
vg0317064370	NA	2.71E-08	mr1700_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
vg0317064370	NA	7.13E-07	mr1727_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
vg0317064370	NA	1.80E-06	mr1785_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
vg0317064370	NA	2.18E-07	mr1804_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
vg0317064370	NA	2.35E-08	mr1837_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
vg0317064370	NA	6.12E-14	mr1938_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
vg0317064370	NA	4.85E-21	mr1945_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