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Detailed information for vg0910828660:

Variant ID: vg0910828660 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10828660
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.04, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

TGGTGACTGGCTTGTGTGCACCTGTGGTTTAGTGTACACCTCACTGCCTTGGCTGCACAGCATGACTCATTAGTTATGGTGCACATGCCCCAAACTGATG[T/C]
TCGTACTTTCCTCACAGGCCTAGATTTGTGTACGGTGATTTGATTTCTGTTTGTGTTATTTTTTGCATGCATGATTTTCAGGGAGTTACACTCGGGTAGG

Reverse complement sequence

CCTACCCGAGTGTAACTCCCTGAAAATCATGCATGCAAAAAATAACACAAACAGAAATCAAATCACCGTACACAAATCTAGGCCTGTGAGGAAAGTACGA[A/G]
CATCAGTTTGGGGCATGTGCACCATAACTAATGAGTCATGCTGTGCAGCCAAGGCAGTGAGGTGTACACTAAACCACAGGTGCACACAAGCCAGTCACCA

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	49.00%	42.70%	0.19%	8.13%	NA
All Indica	2759	80.60%	6.40%	0.33%	12.72%	NA
All Japonica	1512	3.80%	96.20%	0.00%	0.00%	NA
Aus	269	1.90%	87.40%	0.00%	10.78%	NA
Indica I	595	77.60%	11.10%	0.50%	10.76%	NA
Indica II	465	89.70%	8.20%	0.00%	2.15%	NA
Indica III	913	75.90%	1.50%	0.44%	22.12%	NA
Indica Intermediate	786	82.80%	7.40%	0.25%	9.54%	NA
Temperate Japonica	767	4.60%	95.40%	0.00%	0.00%	NA
Tropical Japonica	504	3.60%	96.40%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	4.20%	94.80%	0.00%	1.04%	NA
Intermediate	90	31.10%	65.60%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910828660	T -> DEL	N	N	silent_mutation	Average:37.001; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0910828660	T -> C	LOC_Os09g17720.1	upstream_gene_variant ; 4166.0bp to feature; MODIFIER	silent_mutation	Average:37.001; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0910828660	T -> C	LOC_Os09g17700.1	downstream_gene_variant ; 2410.0bp to feature; MODIFIER	silent_mutation	Average:37.001; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0910828660	T -> C	LOC_Os09g17710.1	downstream_gene_variant ; 1419.0bp to feature; MODIFIER	silent_mutation	Average:37.001; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0910828660	T -> C	LOC_Os09g17700-LOC_Os09g17710	intergenic_region ; MODIFIER	silent_mutation	Average:37.001; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910828660	4.88E-07	4.88E-07	mr1200	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
vg0910828660	NA	2.76E-09	mr1751_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