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Detailed information for vg1009886973:

Variant ID: vg1009886973 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9886973
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGAAGAGACAAGAAATCATGTTTGATAGCCTCACTGGATAATCTTCAAATGCTCGATCGATGGCGGCTACAAGTTCTTCTGTTGTTGTTGAGGCTGATTT[G/A]
TACTGGATGGACTGAATGGAGTTGAAGAAACCCAGATCCAAGACATTCAAATCTGGGGAATTTGCCGGCTGGCAAACAAGTTTGATGTTAAAGCCGTCTT

Reverse complement sequence

AAGACGGCTTTAACATCAAACTTGTTTGCCAGCCGGCAAATTCCCCAGATTTGAATGTCTTGGATCTGGGTTTCTTCAACTCCATTCAGTCCATCCAGTA[C/T]
AAATCAGCCTCAACAACAACAGAAGAACTTGTAGCCGCCATCGATCGAGCATTTGAAGATTATCCAGTGAGGCTATCAAACATGATTTCTTGTCTCTTCA

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	21.80%	14.10%	41.11%	23.02%	NA
All Indica	2759	2.20%	19.30%	60.86%	17.65%	NA
All Japonica	1512	58.30%	4.20%	3.17%	34.33%	NA
Aus	269	0.70%	23.00%	59.85%	16.36%	NA
Indica I	595	1.50%	14.30%	51.09%	33.11%	NA
Indica II	465	1.30%	12.00%	68.39%	18.28%	NA
Indica III	913	2.10%	29.00%	61.45%	7.45%	NA
Indica Intermediate	786	3.30%	16.20%	63.10%	17.43%	NA
Temperate Japonica	767	88.70%	0.50%	0.26%	10.56%	NA
Tropical Japonica	504	12.90%	10.70%	6.94%	69.44%	NA
Japonica Intermediate	241	56.80%	2.10%	4.56%	36.51%	NA
VI/Aromatic	96	55.20%	2.10%	27.08%	15.62%	NA
Intermediate	90	35.60%	6.70%	32.22%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1009886973	G -> A	LOC_Os10g19830.1	synonymous_variant ; p.Tyr361Tyr; LOW	synonymous_codon	Average:19.258; most accessible tissue: Callus, score: 33.415	N	N	N	N
vg1009886973	G -> DEL	LOC_Os10g19830.1	N	frameshift_variant	Average:19.258; most accessible tissue: Callus, score: 33.415	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009886973	NA	2.34E-06	mr1657	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
vg1009886973	NA	6.98E-07	mr1690	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
vg1009886973	4.20E-06	NA	mr1165_2	Jap_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