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Detailed information for vg1009473286:

Variant ID: vg1009473286 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9473286
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGCGGGTGAATCCATTCATTGATAGTGTGGTTTTGTGAAACTACACTACCAAAATATATGTACTTACGTGCTAAGTATCAAAGTGTGTGTGGTTTTATG[T/C]
AACTTGGACTACAAAACGTGAAGTTTTGTGAAATTTACTCTAAAATTAATTACCCATAGACCACGCCGGCGACTACCGGTGACGGCGAAGAACCTCGCAG

Reverse complement sequence

CTGCGAGGTTCTTCGCCGTCACCGGTAGTCGCCGGCGTGGTCTATGGGTAATTAATTTTAGAGTAAATTTCACAAAACTTCACGTTTTGTAGTCCAAGTT[A/G]
CATAAAACCACACACACTTTGATACTTAGCACGTAAGTACATATATTTTGGTAGTGTAGTTTCACAAAACCACACTATCAATGAATGGATTCACCCGCGA

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	56.80%	22.20%	0.08%	20.91%	NA
All Indica	2759	74.40%	2.00%	0.07%	23.49%	NA
All Japonica	1512	15.10%	63.80%	0.13%	20.90%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	97.10%	1.30%	0.00%	1.51%	NA
Indica II	465	77.40%	2.20%	0.00%	20.43%	NA
Indica III	913	54.50%	2.20%	0.11%	43.15%	NA
Indica Intermediate	786	78.50%	2.30%	0.13%	19.08%	NA
Temperate Japonica	767	2.00%	82.90%	0.13%	14.99%	NA
Tropical Japonica	504	36.70%	43.80%	0.20%	19.25%	NA
Japonica Intermediate	241	12.00%	44.80%	0.00%	43.15%	NA
VI/Aromatic	96	85.40%	0.00%	0.00%	14.58%	NA
Intermediate	90	60.00%	30.00%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1009473286	T -> C	LOC_Os10g18660.1	upstream_gene_variant ; 4415.0bp to feature; MODIFIER	silent_mutation	Average:26.287; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg1009473286	T -> C	LOC_Os10g18660-LOC_Os10g18670	intergenic_region ; MODIFIER	silent_mutation	Average:26.287; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg1009473286	T -> DEL	N	N	silent_mutation	Average:26.287; 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
vg1009473286	3.37E-06	8.35E-08	mr1091	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
vg1009473286	NA	9.58E-06	mr1096	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
vg1009473286	NA	1.37E-16	mr1484	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