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Detailed information for vg0509418232:

Variant ID: vg0509418232 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 9418232
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTATATGCTAATTAAGTCTAATTACAAATCTAATAATCTTAATTGCATTACAAATATAACAATCATATATATATATATATATAATTACGTCACTTGCCTG[C/G]
GCGAATTCCTTCGAGGGCTAGCTCTACCACTCCGGCTTGAGGGACGACTCCAACAACGTCTTTTCTGCAAGATACAAAAAGATGTATTAGCATAAACGCG

Reverse complement sequence

CGCGTTTATGCTAATACATCTTTTTGTATCTTGCAGAAAAGACGTTGTTGGAGTCGTCCCTCAAGCCGGAGTGGTAGAGCTAGCCCTCGAAGGAATTCGC[G/C]
CAGGCAAGTGACGTAATTATATATATATATATATATGATTGTTATATTTGTAATGCAATTAAGATTATTAGATTTGTAATTAGACTTAATTAGCATATAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.50%	0.50%	1.27%	0.76%	NA
All Indica	2759	98.60%	0.30%	0.58%	0.62%	NA
All Japonica	1512	98.30%	0.00%	0.46%	1.19%	NA
Aus	269	81.00%	5.20%	13.75%	0.00%	NA
Indica I	595	99.70%	0.20%	0.00%	0.17%	NA
Indica II	465	97.60%	0.00%	0.65%	1.72%	NA
Indica III	913	99.00%	0.40%	0.44%	0.11%	NA
Indica Intermediate	786	97.70%	0.30%	1.15%	0.89%	NA
Temperate Japonica	767	97.50%	0.00%	0.39%	2.09%	NA
Tropical Japonica	504	99.20%	0.00%	0.60%	0.20%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0509418232	C -> DEL	N	N	silent_mutation	Average:26.453; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0509418232	C -> G	LOC_Os05g16600.1	downstream_gene_variant ; 4099.0bp to feature; MODIFIER	silent_mutation	Average:26.453; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0509418232	C -> G	LOC_Os05g16620.1	downstream_gene_variant ; 1494.0bp to feature; MODIFIER	silent_mutation	Average:26.453; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0509418232	C -> G	LOC_Os05g16610.1	intron_variant ; MODIFIER	silent_mutation	Average:26.453; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0509418232	NA	2.69E-06	mr1080	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
vg0509418232	NA	2.04E-06	mr1140	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
vg0509418232	9.92E-07	NA	mr1178	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
vg0509418232	NA	1.38E-06	mr1203	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
vg0509418232	2.48E-06	1.20E-07	mr1395	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
vg0509418232	NA	6.28E-07	mr1618	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