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Detailed information for vg0912925804:

Variant ID: vg0912925804 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 12925804
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAACATTCTATAAATATTTCTAAACCGTTGTGTGTCACTCTTAAATTAGAGATACATTCAATCACTGGTATCCACTTAAATCAATGGACACATTATTTA[C/T]
GTCGTTATTAGATTTTTTTTTCTTTAAAAAAACATCACAAACCTTCTTCCCTTCCACTCCATCCCTATAGGCATTAAAGCACATAAACGCTATGGTAAGT

Reverse complement sequence

ACTTACCATAGCGTTTATGTGCTTTAATGCCTATAGGGATGGAGTGGAAGGGAAGAAGGTTTGTGATGTTTTTTTAAAGAAAAAAAAATCTAATAACGAC[G/A]
TAAATAATGTGTCCATTGATTTAAGTGGATACCAGTGATTGAATGTATCTCTAATTTAAGAGTGACACACAACGGTTTAGAAATATTTATAGAATGTTTA

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	88.10%	9.40%	2.50%	0.00%	NA
All Indica	2759	86.50%	9.40%	4.06%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	40.10%	58.00%	1.86%	0.00%	NA
Indica I	595	90.10%	9.40%	0.50%	0.00%	NA
Indica II	465	89.20%	6.70%	4.09%	0.00%	NA
Indica III	913	82.90%	10.50%	6.57%	0.00%	NA
Indica Intermediate	786	86.40%	9.80%	3.82%	0.00%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	80.20%	19.80%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	1.11%	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
vg0912925804	C -> T	LOC_Os09g21390-LOC_Os09g21410	intergenic_region ; MODIFIER	silent_mutation	Average:23.009; most accessible tissue: Zhenshan97 root, score: 36.298	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0912925804	4.34E-06	4.34E-06	mr1499	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
vg0912925804	NA	5.96E-06	mr1236_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
vg0912925804	NA	5.89E-06	mr1740_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
vg0912925804	NA	2.77E-06	mr1834_2	Ind_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