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Detailed information for vg1019294434:

Variant ID: vg1019294434 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 19294434
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGGTAGTGTTTGGATACAGGGACTTAACTTTAGTTCCTGTATTTAGACACTAATTTAGAGTATTAAATATAAACTACTTATAAAACTAATTACATAAAT[G/A]
AAAGCTAATTCGCGAGACAAATTTTTTAAGCCTAATTAATTCATAATTATAGAATGTTTACTGTATCATCACATAGGCTAATCATGGATTAATTAGGCTC

Reverse complement sequence

GAGCCTAATTAATCCATGATTAGCCTATGTGATGATACAGTAAACATTCTATAATTATGAATTAATTAGGCTTAAAAAATTTGTCTCGCGAATTAGCTTT[C/T]
ATTTATGTAATTAGTTTTATAAGTAGTTTATATTTAATACTCTAAATTAGTGTCTAAATACAGGAACTAAAGTTAAGTCCCTGTATCCAAACACTACCGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	25.70%	0.20%	0.42%	73.72%	NA
All Indica	2759	2.00%	0.00%	0.40%	97.57%	NA
All Japonica	1512	73.30%	0.10%	0.33%	26.32%	NA
Aus	269	0.40%	0.70%	1.49%	97.40%	NA
Indica I	595	4.00%	0.00%	0.50%	95.46%	NA
Indica II	465	1.30%	0.00%	0.22%	98.49%	NA
Indica III	913	0.80%	0.00%	0.22%	99.01%	NA
Indica Intermediate	786	2.30%	0.10%	0.64%	96.95%	NA
Temperate Japonica	767	94.90%	0.00%	0.39%	4.69%	NA
Tropical Japonica	504	35.10%	0.00%	0.20%	64.68%	NA
Japonica Intermediate	241	84.20%	0.40%	0.41%	14.94%	NA
VI/Aromatic	96	29.20%	0.00%	0.00%	70.83%	NA
Intermediate	90	24.40%	4.40%	0.00%	71.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1019294434	G -> A	LOC_Os10g36070-LOC_Os10g36090	intergenic_region ; MODIFIER	silent_mutation	Average:9.036; most accessible tissue: Callus, score: 42.324	N	N	N	N
vg1019294434	G -> DEL	N	N	silent_mutation	Average:9.036; most accessible tissue: Callus, score: 42.324	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1019294434	NA	3.23E-06	mr1181	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
vg1019294434	5.36E-06	NA	mr1731	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
vg1019294434	1.24E-06	1.67E-07	mr1731	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
vg1019294434	NA	7.59E-06	mr1928	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