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Detailed information for vg1020438368:

Variant ID: vg1020438368 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 20438368
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:

TAGTAGAGTACTCTTCTGTTGATTATTACTCCCTTCGTATTTTAATGTATGACGCCGTTGACATTTTAACCAATGTTTGACCATTCGTTTTATTCAAATT[T/A]
TTTATGCAAATAAAAAATACTTATGTCACGCTTAAAGAACATTTAATGATAAATCAAGTCACAATAAAATAAATGATAATTACATAAGTTTTTTGAATAA

Reverse complement sequence

TTATTCAAAAAACTTATGTAATTATCATTTATTTTATTGTGACTTGATTTATCATTAAATGTTCTTTAAGCGTGACATAAGTATTTTTTATTTGCATAAA[A/T]
AATTTGAATAAAACGAATGGTCAAACATTGGTTAAAATGTCAACGGCGTCATACATTAAAATACGAAGGGAGTAATAATCAACAGAAGAGTACTCTACTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	36.90%	0.10%	1.97%	61.02%	NA
All Indica	2759	6.80%	0.20%	1.12%	91.92%	NA
All Japonica	1512	91.80%	0.00%	0.26%	7.94%	NA
Aus	269	44.60%	0.70%	9.29%	45.35%	NA
Indica I	595	13.80%	0.30%	0.84%	85.04%	NA
Indica II	465	5.60%	0.20%	1.72%	92.47%	NA
Indica III	913	2.20%	0.00%	0.99%	96.82%	NA
Indica Intermediate	786	7.50%	0.30%	1.15%	91.09%	NA
Temperate Japonica	767	97.90%	0.00%	0.00%	2.09%	NA
Tropical Japonica	504	81.30%	0.00%	0.79%	17.86%	NA
Japonica Intermediate	241	94.20%	0.00%	0.00%	5.81%	NA
VI/Aromatic	96	8.30%	0.00%	33.33%	58.33%	NA
Intermediate	90	43.30%	0.00%	1.11%	55.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1020438368	T -> A	LOC_Os10g38150.1	upstream_gene_variant ; 2718.0bp to feature; MODIFIER	silent_mutation	Average:43.574; most accessible tissue: Minghui63 root, score: 79.522	N	N	N	N
vg1020438368	T -> A	LOC_Os10g38160.1	intron_variant ; MODIFIER	silent_mutation	Average:43.574; most accessible tissue: Minghui63 root, score: 79.522	N	N	N	N
vg1020438368	T -> DEL	N	N	silent_mutation	Average:43.574; most accessible tissue: Minghui63 root, score: 79.522	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1020438368	9.83E-07	NA	mr1350_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
vg1020438368	NA	7.03E-06	mr1509_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