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Detailed information for vg0904153122:

Variant ID: vg0904153122 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 4153122
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCCAGAAGAGGGCGAGGTAAGAATCAGATAAGCACTTAGGAGGGCAAGGAGCAAGGTAAATAACAACTCAGATAGCACACACTAGGCATAAACTGGATT[C/T]
TTCAAATCATAAAAACACCTACTACAACGGGTGTGGACAAGTCACAGAGCTACGCCGAGCTTGACTGTACGCACACCACCTAGGAGAACCAGACTACCAA

Reverse complement sequence

TTGGTAGTCTGGTTCTCCTAGGTGGTGTGCGTACAGTCAAGCTCGGCGTAGCTCTGTGACTTGTCCACACCCGTTGTAGTAGGTGTTTTTATGATTTGAA[G/A]
AATCCAGTTTATGCCTAGTGTGTGCTATCTGAGTTGTTATTTACCTTGCTCCTTGCCCTCCTAAGTGCTTATCTGATTCTTACCTCGCCCTCTTCTGGGA

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	58.60%	0.10%	13.75%	27.57%	NA
All Indica	2759	33.20%	0.20%	22.15%	44.51%	NA
All Japonica	1512	98.80%	0.00%	0.46%	0.73%	NA
Aus	269	81.40%	0.00%	6.32%	12.27%	NA
Indica I	595	15.50%	0.30%	19.16%	65.04%	NA
Indica II	465	32.70%	0.20%	22.15%	44.95%	NA
Indica III	913	42.20%	0.20%	26.94%	30.67%	NA
Indica Intermediate	786	36.40%	0.00%	18.83%	44.78%	NA
Temperate Japonica	767	98.60%	0.00%	0.39%	1.04%	NA
Tropical Japonica	504	99.00%	0.00%	0.60%	0.40%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	71.90%	0.00%	10.42%	17.71%	NA
Intermediate	90	78.90%	0.00%	5.56%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0904153122	C -> DEL	N	N	silent_mutation	Average:33.567; most accessible tissue: Zhenshan97 flag leaf, score: 83.684	N	N	N	N
vg0904153122	C -> T	LOC_Os09g08040.1	upstream_gene_variant ; 500.0bp to feature; MODIFIER	silent_mutation	Average:33.567; most accessible tissue: Zhenshan97 flag leaf, score: 83.684	N	N	N	N
vg0904153122	C -> T	LOC_Os09g08050.1	downstream_gene_variant ; 210.0bp to feature; MODIFIER	silent_mutation	Average:33.567; most accessible tissue: Zhenshan97 flag leaf, score: 83.684	N	N	N	N
vg0904153122	C -> T	LOC_Os09g08040-LOC_Os09g08050	intergenic_region ; MODIFIER	silent_mutation	Average:33.567; most accessible tissue: Zhenshan97 flag leaf, score: 83.684	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0904153122	2.18E-06	NA	mr1301_2	Ind_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
vg0904153122	3.92E-06	3.92E-06	mr1537_2	Ind_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