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Detailed information for vg0316492889:

Variant ID: vg0316492889 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 16492889
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

AAAATTTTTCTACTGCGTAAACCAGGAACCATGCAAGTATTAGATCATAGATCGTTACCACTCGACGCGCTGCGCAGCGGAAGAAGACGCTAAGAAGTCG[A/G]
AGGAACTCTCGCGAAGTAGCGCGCGTCGATGTAGAGGAAGTAGTCGATCGCACCGGCCCGACCATCTCCTCCTCGTGCGTTCTCCTCGCCGTACTCCCAC

Reverse complement sequence

GTGGGAGTACGGCGAGGAGAACGCACGAGGAGGAGATGGTCGGGCCGGTGCGATCGACTACTTCCTCTACATCGACGCGCGCTACTTCGCGAGAGTTCCT[T/C]
CGACTTCTTAGCGTCTTCTTCCGCTGCGCAGCGCGTCGAGTGGTAACGATCTATGATCTAATACTTGCATGGTTCCTGGTTTACGCAGTAGAAAAATTTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.20%	10.00%	0.53%	10.26%	NA
All Indica	2759	96.80%	0.30%	0.47%	2.43%	NA
All Japonica	1512	43.40%	30.20%	0.60%	25.79%	NA
Aus	269	92.90%	0.00%	1.12%	5.95%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	97.80%	0.20%	0.43%	1.51%	NA
Indica III	913	95.50%	0.10%	1.10%	3.29%	NA
Indica Intermediate	786	95.30%	0.80%	0.13%	3.82%	NA
Temperate Japonica	767	54.10%	4.60%	0.52%	40.81%	NA
Tropical Japonica	504	28.80%	62.90%	0.40%	7.94%	NA
Japonica Intermediate	241	39.80%	43.60%	1.24%	15.35%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	81.10%	10.00%	0.00%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0316492889	A -> DEL	N	N	silent_mutation	Average:54.553; most accessible tissue: Zhenshan97 flag leaf, score: 84.585	N	N	N	N
vg0316492889	A -> G	LOC_Os03g29035.1	intron_variant ; MODIFIER	silent_mutation	Average:54.553; most accessible tissue: Zhenshan97 flag leaf, score: 84.585	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0316492889	NA	1.78E-06	mr1401	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
vg0316492889	NA	9.33E-06	mr1852	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
vg0316492889	1.62E-06	6.81E-09	mr1020_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
vg0316492889	NA	7.19E-06	mr1220_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
vg0316492889	NA	3.42E-06	mr1269_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
vg0316492889	NA	1.11E-06	mr1470_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
vg0316492889	NA	1.33E-06	mr1479_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
vg0316492889	NA	2.09E-08	mr1502_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
vg0316492889	NA	2.92E-06	mr1546_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
vg0316492889	NA	5.67E-06	mr1596_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
vg0316492889	NA	4.02E-10	mr1680_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
vg0316492889	NA	1.43E-07	mr1765_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
vg0316492889	NA	8.74E-09	mr1786_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