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Detailed information for vg0121586179:

Variant ID: vg0121586179 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 21586179
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, T: 0.02, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

ACTCCAGGAGCCGCTCAGAGGGACCTAGCGACGAGCAGGAGGACGCCTTCGACTCCACCGACCGCAGGAGCCGTTCCGAGCATTAGGCTCGTTTTCCCTT[T/A]
GTTTATCGACTGCTTAGTAATTGCCTGTTAGTTTGTGTGTCTAGGTTTGTTCGCTTGTGGGTCAGTCGACGGTCGATATCATGTGCCTATGATATGGCTG

Reverse complement sequence

CAGCCATATCATAGGCACATGATATCGACCGTCGACTGACCCACAAGCGAACAAACCTAGACACACAAACTAACAGGCAATTACTAAGCAGTCGATAAAC[A/T]
AAGGGAAAACGAGCCTAATGCTCGGAACGGCTCCTGCGGTCGGTGGAGTCGAAGGCGTCCTCCTGCTCGTCGCTAGGTCCCTCTGAGCGGCTCCTGGAGT

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	34.80%	11.80%	45.30%	8.10%	NA
All Indica	2759	4.30%	19.50%	69.66%	6.49%	NA
All Japonica	1512	92.50%	0.30%	2.71%	4.56%	NA
Aus	269	5.60%	1.10%	51.67%	41.64%	NA
Indica I	595	3.90%	6.20%	78.99%	10.92%	NA
Indica II	465	4.30%	21.50%	65.81%	8.39%	NA
Indica III	913	2.20%	30.40%	66.37%	0.99%	NA
Indica Intermediate	786	7.10%	15.80%	68.70%	8.40%	NA
Temperate Japonica	767	96.10%	0.00%	0.78%	3.13%	NA
Tropical Japonica	504	88.10%	0.80%	5.95%	5.16%	NA
Japonica Intermediate	241	90.00%	0.00%	2.07%	7.88%	NA
VI/Aromatic	96	66.70%	4.20%	12.50%	16.67%	NA
Intermediate	90	55.60%	6.70%	30.00%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0121586179	T -> A	LOC_Os01g38420.1	upstream_gene_variant ; 1109.0bp to feature; MODIFIER	silent_mutation	Average:38.12; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0121586179	T -> A	LOC_Os01g38410.1	intron_variant ; MODIFIER	silent_mutation	Average:38.12; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0121586179	T -> DEL	N	N	silent_mutation	Average:38.12; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0121586179	2.84E-06	NA	mr1593_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