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Detailed information for vg1104837937:

Variant ID: vg1104837937 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 4837937
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAGCGAATGTCCACTTGATTAATAAATCTAAGGGATTGTTTCTTCGGCACCTAACTATCAATCTGACCCTATTTTTGTAGTTTGCTCATTGGACCATGC[T/A]
TTTTAAAAACGAAGAGTACCCTCTTCCGTTAAGGCAACGTAATGACATTAATTCAGGGCAAAATGGCTTATATGAAAATGCAGTCAAGTTGGAGCTCCGC

Reverse complement sequence

GCGGAGCTCCAACTTGACTGCATTTTCATATAAGCCATTTTGCCCTGAATTAATGTCATTACGTTGCCTTAACGGAAGAGGGTACTCTTCGTTTTTAAAA[A/T]
GCATGGTCCAATGAGCAAACTACAAAAATAGGGTCAGATTGATAGTTAGGTGCCGAAGAAACAATCCCTTAGATTTATTAATCAAGTGGACATTCGCTTG

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	86.00%	14.00%	0.02%	0.00%	NA
All Indica	2759	80.60%	19.40%	0.04%	0.00%	NA
All Japonica	1512	94.80%	5.20%	0.00%	0.00%	NA
Aus	269	84.00%	16.00%	0.00%	0.00%	NA
Indica I	595	97.80%	2.20%	0.00%	0.00%	NA
Indica II	465	96.60%	3.40%	0.00%	0.00%	NA
Indica III	913	55.30%	44.70%	0.00%	0.00%	NA
Indica Intermediate	786	87.50%	12.30%	0.13%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	87.30%	12.70%	0.00%	0.00%	NA
Japonica Intermediate	241	94.60%	5.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg1104837937	T -> A	LOC_Os11g09100-LOC_Os11g09110	intergenic_region ; MODIFIER	silent_mutation	Average:45.589; most accessible tissue: Callus, score: 62.096	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1104837937	2.06E-06	2.63E-06	mr1240_2	Ind_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
vg1104837937	8.76E-06	NA	mr1496_2	Ind_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