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Detailed information for vg1009180380:

Variant ID: vg1009180380 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9180380
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATTACAGTTTCCGCCAGGAAACTGCGAGACGAATTTATTAAGCCTAATTAATCCGTCATTAGCAAATATTTACTGTAGCACCATATTGTTAAATCATGG[C/T]
GCAATTAGGCTTAAAAGATTCGTCTCGTAATTTACACGCAATATATGTAATTGGTTTTTCCTTTTGTCTACATGTTATATTCCACACATGTGTCTAAACA

Reverse complement sequence

TGTTTAGACACATGTGTGGAATATAACATGTAGACAAAAGGAAAAACCAATTACATATATTGCGTGTAAATTACGAGACGAATCTTTTAAGCCTAATTGC[G/A]
CCATGATTTAACAATATGGTGCTACAGTAAATATTTGCTAATGACGGATTAATTAGGCTTAATAAATTCGTCTCGCAGTTTCCTGGCGGAAACTGTAATT

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	93.10%	5.00%	1.71%	0.28%	NA
All Indica	2759	99.70%	0.10%	0.07%	0.11%	NA
All Japonica	1512	79.20%	15.00%	5.16%	0.60%	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	99.60%	0.20%	0.22%	0.00%	NA
Indica III	913	99.80%	0.10%	0.00%	0.11%	NA
Indica Intermediate	786	99.60%	0.00%	0.13%	0.25%	NA
Temperate Japonica	767	63.10%	28.90%	7.95%	0.00%	NA
Tropical Japonica	504	98.40%	0.00%	0.20%	1.39%	NA
Japonica Intermediate	241	90.50%	2.10%	6.64%	0.83%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	5.60%	1.11%	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
vg1009180380	C -> T	LOC_Os10g18099.1	upstream_gene_variant ; 4245.0bp to feature; MODIFIER	silent_mutation	Average:31.888; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1009180380	C -> T	LOC_Os10g18090-LOC_Os10g18099	intergenic_region ; MODIFIER	silent_mutation	Average:31.888; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1009180380	C -> DEL	N	N	silent_mutation	Average:31.888; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009180380	NA	1.86E-06	mr1768	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
vg1009180380	NA	8.87E-09	mr1768_2	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