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Detailed information for vg1019855130:

Variant ID: vg1019855130 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 19855130
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.71, G: 0.29, others allele: 0.00, population size: 154. )

Flanking Sequence (100 bp) in Reference Genome:

GTCCATACCAGCCGTTCACATCACAACCCTTTGAATCTGACGCAAGTCACCACCAAGTCAACCAAGGCAATAGGCTGTATATCTTCACACCATCCATCTA[G/T]
TCTCTCTCTCCTCACATGGCTGCCACGCACAGGATCATAGCAGAGAGAGACACCGAGAGACAGTGGAGAAGAACAACCTGTCAACAGGTTTGTGTGGTGG

Reverse complement sequence

CCACCACACAAACCTGTTGACAGGTTGTTCTTCTCCACTGTCTCTCGGTGTCTCTCTCTGCTATGATCCTGTGCGTGGCAGCCATGTGAGGAGAGAGAGA[C/A]
TAGATGGATGGTGTGAAGATATACAGCCTATTGCCTTGGTTGACTTGGTGGTGACTTGCGTCAGATTCAAAGGGTTGTGATGTGAACGGCTGGTATGGAC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	31.20%	16.10%	2.56%	50.19%	NA
All Indica	2759	13.60%	17.70%	3.84%	64.95%	NA
All Japonica	1512	69.80%	0.70%	0.40%	29.10%	NA
Aus	269	1.90%	77.70%	1.49%	18.96%	NA
Indica I	595	23.50%	9.90%	4.03%	62.52%	NA
Indica II	465	8.20%	13.50%	4.52%	73.76%	NA
Indica III	913	14.50%	22.70%	3.72%	59.15%	NA
Indica Intermediate	786	8.10%	20.10%	3.44%	68.32%	NA
Temperate Japonica	767	90.20%	0.50%	0.13%	9.13%	NA
Tropical Japonica	504	31.70%	0.60%	0.79%	66.87%	NA
Japonica Intermediate	241	84.60%	1.20%	0.41%	13.69%	NA
VI/Aromatic	96	8.30%	44.80%	3.12%	43.75%	NA
Intermediate	90	33.30%	12.20%	2.22%	52.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1019855130	G -> T	LOC_Os10g37090.1	missense_variant ; p.Leu98Ile; MODERATE	nonsynonymous_codon ; L98I	Average:15.813; most accessible tissue: Callus, score: 94.922	unknown	unknown	TOLERATED	0.72
vg1019855130	G -> DEL	LOC_Os10g37090.1	N	frameshift_variant	Average:15.813; most accessible tissue: Callus, score: 94.922	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1019855130	NA	5.47E-09	mr1248	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
vg1019855130	NA	9.44E-08	mr1030_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
vg1019855130	NA	4.07E-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
vg1019855130	NA	8.26E-07	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
vg1019855130	NA	2.47E-07	mr1555_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
vg1019855130	NA	8.78E-06	mr1623_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
vg1019855130	NA	6.04E-07	mr1754_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
vg1019855130	2.37E-06	2.33E-07	mr1965_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