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Detailed information for vg1018035120:

Variant ID: vg1018035120 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 18035120
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTTCATCACTTGGATTGACGTTTAATTATAATAAGAAAGTACCCAACTGTCCTTGTTCTATTGGCTAATCGGAGACTATATCTTTGCAGGCTAAGCCGC[C/T]
GCAGTAACCGCATGCACTCAATAGGTAACTATCGTCTTATAATGTACTCCCTCTCTAAAATAAACAAAATTCTAGAAATGTTATAATCAAGTTTTTCTAA

Reverse complement sequence

TTAGAAAAACTTGATTATAACATTTCTAGAATTTTGTTTATTTTAGAGAGGGAGTACATTATAAGACGATAGTTACCTATTGAGTGCATGCGGTTACTGC[G/A]
GCGGCTTAGCCTGCAAAGATATAGTCTCCGATTAGCCAATAGAACAAGGACAGTTGGGTACTTTCTTATTATAATTAAACGTCAATCCAAGTGATGAAGA

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	99.40%	0.40%	0.15%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	98.20%	1.30%	0.46%	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	97.30%	2.00%	0.78%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg1018035120	C -> T	LOC_Os10g33930.1	upstream_gene_variant ; 1427.0bp to feature; MODIFIER	silent_mutation	Average:40.501; most accessible tissue: Zhenshan97 flower, score: 49.187	N	N	N	N
vg1018035120	C -> T	LOC_Os10g33920-LOC_Os10g33930	intergenic_region ; MODIFIER	silent_mutation	Average:40.501; most accessible tissue: Zhenshan97 flower, score: 49.187	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1018035120	4.82E-07	1.88E-07	mr1240	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
vg1018035120	NA	2.37E-06	mr1496	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