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Detailed information for vg0819105437:

Variant ID: vg0819105437 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 19105437
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGAGAAACCACAGCATAGTGGATAGAATGTGAATCGGCTAACGCAGGATCATGTTGCAGCTATGTTCTTATCTCCTCAACCTACTGTTGATCCAACCCAG[C/T]
AGCAGCCGATTCAGCAAATACCACCAAGGCAGCAGGTTGTACAGCCGATTCAACAAACACCACCAATCCAACAGGTTGTGCAACCAATTCAGCAGACGCC

Reverse complement sequence

GGCGTCTGCTGAATTGGTTGCACAACCTGTTGGATTGGTGGTGTTTGTTGAATCGGCTGTACAACCTGCTGCCTTGGTGGTATTTGCTGAATCGGCTGCT[G/A]
CTGGGTTGGATCAACAGTAGGTTGAGGAGATAAGAACATAGCTGCAACATGATCCTGCGTTAGCCGATTCACATTCTATCCACTATGCTGTGGTTTCTCT

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	43.00%	5.00%	11.72%	40.33%	NA
All Indica	2759	22.30%	0.30%	14.39%	63.07%	NA
All Japonica	1512	73.50%	14.90%	4.70%	6.94%	NA
Aus	269	59.50%	0.40%	29.37%	10.78%	NA
Indica I	595	15.00%	0.80%	18.66%	65.55%	NA
Indica II	465	16.30%	0.00%	11.83%	71.83%	NA
Indica III	913	27.90%	0.00%	13.03%	59.04%	NA
Indica Intermediate	786	24.70%	0.40%	14.25%	60.69%	NA
Temperate Japonica	767	71.20%	19.90%	7.82%	1.04%	NA
Tropical Japonica	504	82.90%	3.40%	0.79%	12.90%	NA
Japonica Intermediate	241	61.00%	22.80%	2.90%	13.28%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	55.60%	2.20%	7.78%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0819105437	C -> T	LOC_Os08g30940.1	stop_gained ; p.Gln218*; HIGH	stop_gained	Average:9.059; most accessible tissue: Callus, score: 25.379	N	N	N	N
vg0819105437	C -> DEL	LOC_Os08g30940.1	N	frameshift_variant	Average:9.059; most accessible tissue: Callus, score: 25.379	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0819105437	NA	9.49E-06	mr1329_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
vg0819105437	NA	1.18E-06	mr1524_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
vg0819105437	1.95E-06	NA	mr1645_2	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
vg0819105437	1.74E-07	NA	mr1647_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
vg0819105437	2.04E-06	NA	mr1657_2	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