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Detailed information for vg0918827520:

Variant ID: vg0918827520 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 18827520
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTAGTGTAACATTGTCACGCCCAGAAATTCCCGAATAGAATTCCAAGCAGAATGTGCATTAAAATCCCCGTCCAGGACCAGCCGGGGTACACAAACGACA[G/A]
TGTTGACATTCAGATCCACGTCTTACAAACATCATAAAAGATTACAAATGCAGCGGAAAAAGATAAAAGCGAGCTAAGCCTGAAGGCTTGACTCCTGCAG

Reverse complement sequence

CTGCAGGAGTCAAGCCTTCAGGCTTAGCTCGCTTTTATCTTTTTCCGCTGCATTTGTAATCTTTTATGATGTTTGTAAGACGTGGATCTGAATGTCAACA[C/T]
TGTCGTTTGTGTACCCCGGCTGGTCCTGGACGGGGATTTTAATGCACATTCTGCTTGGAATTCTATTCGGGAATTTCTGGGCGTGACAATGTTACACTAA

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	28.00%	0.40%	5.44%	66.19%	NA
All Indica	2759	3.10%	0.40%	5.76%	90.69%	NA
All Japonica	1512	77.10%	0.10%	3.17%	19.64%	NA
Aus	269	3.70%	1.50%	10.78%	84.01%	NA
Indica I	595	3.00%	0.00%	0.67%	96.30%	NA
Indica II	465	3.90%	0.40%	2.37%	93.33%	NA
Indica III	913	1.30%	0.80%	10.62%	87.29%	NA
Indica Intermediate	786	4.80%	0.40%	5.98%	88.80%	NA
Temperate Japonica	767	70.90%	0.00%	2.74%	26.34%	NA
Tropical Japonica	504	88.50%	0.20%	1.39%	9.92%	NA
Japonica Intermediate	241	73.00%	0.00%	8.30%	18.67%	NA
VI/Aromatic	96	17.70%	1.00%	11.46%	69.79%	NA
Intermediate	90	48.90%	0.00%	11.11%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0918827520	G -> DEL	N	N	silent_mutation	Average:35.085; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N
vg0918827520	G -> A	LOC_Os09g31310.1	upstream_gene_variant ; 1258.0bp to feature; MODIFIER	silent_mutation	Average:35.085; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N
vg0918827520	G -> A	LOC_Os09g31310-LOC_Os09g31330	intergenic_region ; MODIFIER	silent_mutation	Average:35.085; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0918827520	NA	4.09E-16	mr1164	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
vg0918827520	NA	2.14E-11	mr1172	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
vg0918827520	NA	1.11E-60	mr1246	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
vg0918827520	NA	1.20E-07	mr1249	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
vg0918827520	2.84E-06	1.18E-06	mr1322	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
vg0918827520	NA	1.52E-12	mr1326	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
vg0918827520	NA	1.28E-23	mr1571	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
vg0918827520	NA	9.67E-19	mr1598	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
vg0918827520	8.95E-06	8.15E-06	mr1712	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
vg0918827520	5.75E-07	NA	mr1719	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
vg0918827520	5.03E-09	5.47E-09	mr1719	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
vg0918827520	NA	8.57E-13	mr1514_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
vg0918827520	NA	1.88E-33	mr1598_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
vg0918827520	NA	1.37E-07	mr1676_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