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Detailed information for vg1008554925:

Variant ID: vg1008554925 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 8554925
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGATCCCAAACAACCCTTTGAGCATGTTGAACCCGTTTAAAGCTATTGTTTGATTTCAACTTATGCATTATTTTCGAATGTCATCGGGTGGTGAGCCTTT[C/T]
CCAATTAATTAATGGCCGAAGATGACTTTATTTTCCTATTAGCTAGAACCTTATATATTAGTTTGGGTTCAGCTAAATGCTATATATATATAATTGCTTA

Reverse complement sequence

TAAGCAATTATATATATATAGCATTTAGCTGAACCCAAACTAATATATAAGGTTCTAGCTAATAGGAAAATAAAGTCATCTTCGGCCATTAATTAATTGG[G/A]
AAAGGCTCACCACCCGATGACATTCGAAAATAATGCATAAGTTGAAATCAAACAATAGCTTTAAACGGGTTCAACATGCTCAAAGGGTTGTTTGGGATCT

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	94.90%	2.00%	3.05%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	84.30%	6.30%	9.33%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	71.30%	11.20%	17.47%	0.00%	NA
Tropical Japonica	504	98.60%	0.40%	0.99%	0.00%	NA
Japonica Intermediate	241	95.90%	3.30%	0.83%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	97.80%	0.00%	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
vg1008554925	C -> T	LOC_Os10g17070.1	upstream_gene_variant ; 1703.0bp to feature; MODIFIER	silent_mutation	Average:55.399; most accessible tissue: Zhenshan97 flag leaf, score: 74.162	N	N	N	N
vg1008554925	C -> T	LOC_Os10g17080.1	downstream_gene_variant ; 1258.0bp to feature; MODIFIER	silent_mutation	Average:55.399; most accessible tissue: Zhenshan97 flag leaf, score: 74.162	N	N	N	N
vg1008554925	C -> T	LOC_Os10g17070-LOC_Os10g17080	intergenic_region ; MODIFIER	silent_mutation	Average:55.399; most accessible tissue: Zhenshan97 flag leaf, score: 74.162	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1008554925	NA	3.79E-08	mr1062	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
vg1008554925	2.87E-07	2.87E-07	mr1950	Jap_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