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Detailed information for vg0907046341:

Variant ID: vg0907046341 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7046341
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.84, T: 0.16, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

AAATGCCCGTGCGTTACAACGGGTGAAGAGTATTTTAATCTTATTATTGTTGTACGGTTTAGCTAAGGTGAAATTCACCGTAGGAATTCACTTGGATATT[C/T]
TTTTTATAAAATCATAAGCCGCAATTAGGGGTTCGATCATCTCAAGTTAGCATGCAAGTTTGTTAAAGAGATTTCTTATACGACTCCTTCTATATTTCTA

Reverse complement sequence

TAGAAATATAGAAGGAGTCGTATAAGAAATCTCTTTAACAAACTTGCATGCTAACTTGAGATGATCGAACCCCTAATTGCGGCTTATGATTTTATAAAAA[G/A]
AATATCCAAGTGAATTCCTACGGTGAATTTCACCTTAGCTAAACCGTACAACAATAATAAGATTAAAATACTCTTCACCCGTTGTAACGCACGGGCATTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.80%	45.00%	0.13%	0.00%	NA
All Indica	2759	88.60%	11.20%	0.22%	0.00%	NA
All Japonica	1512	1.70%	98.30%	0.00%	0.00%	NA
Aus	269	19.00%	81.00%	0.00%	0.00%	NA
Indica I	595	79.70%	19.80%	0.50%	0.00%	NA
Indica II	465	90.50%	9.50%	0.00%	0.00%	NA
Indica III	913	96.30%	3.70%	0.00%	0.00%	NA
Indica Intermediate	786	85.20%	14.40%	0.38%	0.00%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	1.20%	98.80%	0.00%	0.00%	NA
Japonica Intermediate	241	6.60%	93.40%	0.00%	0.00%	NA
VI/Aromatic	96	40.60%	59.40%	0.00%	0.00%	NA
Intermediate	90	36.70%	63.30%	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
vg0907046341	C -> T	LOC_Os09g12350.1	intron_variant ; MODIFIER	silent_mutation	Average:33.581; most accessible tissue: Minghui63 root, score: 59.105	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907046341	NA	3.09E-12	mr1034	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
vg0907046341	4.34E-07	4.34E-07	mr1905	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