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Detailed information for vg0105937313:

Variant ID: vg0105937313 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 5937313
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATAAAAACAATAACCCCAGAAATTGCAGTACTTGATATTGTACACAATATAAGCAAAAAAAAAACCGAATAACCAAAATAGTTTCATTTCCTTTCTTAA[T/A]
AACAAGAAAAAAATTACTAATAGAAGAGATGTTGGGTTTTTATTCTAACATACAAATGCACTCACCCTTTGTCACTCATGTACTTACAGTTTAGAGCATA

Reverse complement sequence

TATGCTCTAAACTGTAAGTACATGAGTGACAAAGGGTGAGTGCATTTGTATGTTAGAATAAAAACCCAACATCTCTTCTATTAGTAATTTTTTTCTTGTT[A/T]
TTAAGAAAGGAAATGAAACTATTTTGGTTATTCGGTTTTTTTTTTGCTTATATTGTGTACAATATCAAGTACTGCAATTTCTGGGGTTATTGTTTTTATT

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	95.50%	3.30%	1.27%	0.00%	NA
All Indica	2759	99.20%	0.30%	0.58%	0.00%	NA
All Japonica	1512	88.60%	8.50%	2.91%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.00%	0.80%	2.18%	0.00%	NA
Indica II	465	99.60%	0.20%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.10%	0.25%	0.00%	NA
Temperate Japonica	767	78.90%	15.60%	5.48%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	2.50%	0.83%	0.00%	NA
VI/Aromatic	96	82.30%	17.70%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0105937313	T -> A	LOC_Os01g11110.2	downstream_gene_variant ; 3127.0bp to feature; MODIFIER	silent_mutation	Average:45.521; most accessible tissue: Callus, score: 80.898	N	N	N	N
vg0105937313	T -> A	LOC_Os01g11120.1	intron_variant ; MODIFIER	silent_mutation	Average:45.521; most accessible tissue: Callus, score: 80.898	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0105937313	NA	4.22E-06	mr1321_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
vg0105937313	2.56E-06	4.60E-08	mr1576_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