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Detailed information for vg1009535675:

Variant ID: vg1009535675 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9535675
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACACAAGCCGGTCTGACCGGCAACCACCGCCTTTTCTGACCGGTCCTGACAAAACAGCAAACCCTGTTCATCACCTGAAAATTAATTATCTCCAAAACCA[C/T]
TTCGACACTAATCTCCAAATATCAAAACCAATAATCACAGATGCCAATTATTCATCATAGAAGAAGAATCAAAACACATGTTGATCTTACAATATTCCAG

Reverse complement sequence

CTGGAATATTGTAAGATCAACATGTGTTTTGATTCTTCTTCTATGATGAATAATTGGCATCTGTGATTATTGGTTTTGATATTTGGAGATTAGTGTCGAA[G/A]
TGGTTTTGGAGATAATTAATTTTCAGGTGATGAACAGGGTTTGCTGTTTTGTCAGGACCGGTCAGAAAAGGCGGTGGTTGCCGGTCAGACCGGCTTGTGT

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	90.10%	6.50%	0.13%	3.24%	NA
All Indica	2759	97.80%	2.10%	0.00%	0.04%	NA
All Japonica	1512	81.90%	8.30%	0.40%	9.33%	NA
Aus	269	64.30%	35.70%	0.00%	0.00%	NA
Indica I	595	98.30%	1.50%	0.00%	0.17%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	98.10%	1.90%	0.00%	0.00%	NA
Indica Intermediate	786	95.90%	4.10%	0.00%	0.00%	NA
Temperate Japonica	767	87.70%	0.40%	0.65%	11.21%	NA
Tropical Japonica	504	77.60%	21.20%	0.00%	1.19%	NA
Japonica Intermediate	241	72.60%	6.60%	0.41%	20.33%	NA
VI/Aromatic	96	69.80%	20.80%	0.00%	9.38%	NA
Intermediate	90	88.90%	8.90%	0.00%	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
vg1009535675	C -> T	LOC_Os10g18740.1	upstream_gene_variant ; 3127.0bp to feature; MODIFIER	silent_mutation	Average:44.832; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg1009535675	C -> T	LOC_Os10g18750.1	intron_variant ; MODIFIER	silent_mutation	Average:44.832; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg1009535675	C -> DEL	N	N	silent_mutation	Average:44.832; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009535675	1.65E-06	NA	mr1379	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
vg1009535675	NA	8.30E-06	mr1808	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
vg1009535675	NA	3.09E-07	mr1815	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
vg1009535675	NA	3.35E-06	mr1815_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