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Detailed information for vg0518987917:

Variant ID: vg0518987917 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 18987917
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAATACTATGGTGCCCCTCATTAAATGGTGTTTATGTGAGAGTGGAAAGATGGCTGAGGGTAAAATAGGGAGAAATTTAAATGAGAAATGATTGATGGGG[T/C]
AATTAGTACTCTAGAATTACAATTATTTTGGGATGAATTTTCAATCCTAGAAATATAATTATTTTGGGACGGAGGTAGTACTATTCATCATTGATGAGGA

Reverse complement sequence

TCCTCATCAATGATGAATAGTACTACCTCCGTCCCAAAATAATTATATTTCTAGGATTGAAAATTCATCCCAAAATAATTGTAATTCTAGAGTACTAATT[A/G]
CCCCATCAATCATTTCTCATTTAAATTTCTCCCTATTTTACCCTCAGCCATCTTTCCACTCTCACATAAACACCATTTAATGAGGGGCACCATAGTATTT

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	69.50%	30.10%	0.23%	0.13%	NA
All Indica	2759	98.40%	1.10%	0.33%	0.22%	NA
All Japonica	1512	15.70%	84.20%	0.07%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	98.30%	1.50%	0.22%	0.00%	NA
Indica III	913	97.90%	1.10%	0.44%	0.55%	NA
Indica Intermediate	786	98.10%	1.30%	0.51%	0.13%	NA
Temperate Japonica	767	4.80%	95.00%	0.13%	0.00%	NA
Tropical Japonica	504	33.30%	66.70%	0.00%	0.00%	NA
Japonica Intermediate	241	13.70%	86.30%	0.00%	0.00%	NA
VI/Aromatic	96	7.30%	92.70%	0.00%	0.00%	NA
Intermediate	90	65.60%	33.30%	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
vg0518987917	T -> DEL	N	N	silent_mutation	Average:57.032; most accessible tissue: Zhenshan97 root, score: 83.907	N	N	N	N
vg0518987917	T -> C	LOC_Os05g32490-LOC_Os05g32500	intergenic_region ; MODIFIER	silent_mutation	Average:57.032; most accessible tissue: Zhenshan97 root, score: 83.907	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0518987917	4.45E-07	NA	mr1301	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
vg0518987917	3.65E-13	3.76E-14	mr1410	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
vg0518987917	1.08E-07	1.14E-13	mr1410	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
vg0518987917	3.45E-08	NA	mr1301_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
vg0518987917	4.92E-16	1.82E-13	mr1410_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
vg0518987917	2.39E-09	6.56E-14	mr1410_2	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