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Detailed information for vg0121350313:

Variant ID: vg0121350313 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 21350313
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.89, T: 0.12, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

CTCCCTCTGTTTTTTCTCTATTTGACATTGAACTAACCAACATCAGAAGTTTGGAAACATAGACATTATTAATTATTTGCTACATTTCATTCATCTAAAA[A/T]
TTTTTAATTTTGAAATCACCTAAAACTACATGCTTCTAAACAGGGAGGAACGTAGCATCAAACTAGAAGTGCTCATCTTTTTCTTCATCTTTTGGCTCCC

Reverse complement sequence

GGGAGCCAAAAGATGAAGAAAAAGATGAGCACTTCTAGTTTGATGCTACGTTCCTCCCTGTTTAGAAGCATGTAGTTTTAGGTGATTTCAAAATTAAAAA[T/A]
TTTTAGATGAATGAAATGTAGCAAATAATTAATAATGTCTATGTTTCCAAACTTCTGATGTTGGTTAGTTCAATGTCAAATAGAGAAAAAACAGAGGGAG

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	59.80%	40.20%	0.02%	0.00%	NA
All Indica	2759	93.10%	6.80%	0.04%	0.00%	NA
All Japonica	1512	1.10%	98.90%	0.00%	0.00%	NA
Aus	269	57.20%	42.80%	0.00%	0.00%	NA
Indica I	595	99.30%	0.50%	0.17%	0.00%	NA
Indica II	465	95.70%	4.30%	0.00%	0.00%	NA
Indica III	913	95.10%	4.90%	0.00%	0.00%	NA
Indica Intermediate	786	84.70%	15.30%	0.00%	0.00%	NA
Temperate Japonica	767	1.00%	99.00%	0.00%	0.00%	NA
Tropical Japonica	504	0.80%	99.20%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	50.00%	50.00%	0.00%	0.00%	NA
Intermediate	90	40.00%	60.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0121350313	A -> T	LOC_Os01g38120.1	upstream_gene_variant ; 639.0bp to feature; MODIFIER	silent_mutation	Average:54.318; most accessible tissue: Callus, score: 80.173	N	N	N	N
vg0121350313	A -> T	LOC_Os01g38140.1	upstream_gene_variant ; 4157.0bp to feature; MODIFIER	silent_mutation	Average:54.318; most accessible tissue: Callus, score: 80.173	N	N	N	N
vg0121350313	A -> T	LOC_Os01g38130.1	intron_variant ; MODIFIER	silent_mutation	Average:54.318; most accessible tissue: Callus, score: 80.173	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0121350313	NA	1.37E-61	mr1125_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