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Detailed information for vg1121848527:

Variant ID: vg1121848527 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21848527
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTCGGGCACGGGCATCGGAACACCTCCCCTCAAATTTAAAATATCCGACGATGGGTAAAACTTGGGGTTTTACAAAAGACTTGGAAAACCCAACACCTG[G/A]
GTCGGTGCTTGTGAACTAAATGAATTTCCAAAACCGCAGACCGGGGGACGAACCGGGAGTACGGTTTCCCGCTCTTGCACTTAAGGACCGTTTCCCTTGG

Reverse complement sequence

CCAAGGGAAACGGTCCTTAAGTGCAAGAGCGGGAAACCGTACTCCCGGTTCGTCCCCCGGTCTGCGGTTTTGGAAATTCATTTAGTTCACAAGCACCGAC[C/T]
CAGGTGTTGGGTTTTCCAAGTCTTTTGTAAAACCCCAAGTTTTACCCATCGTCGGATATTTTAAATTTGAGGGGAGGTGTTCCGATGCCCGTGCCCGAAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	27.80%	0.20%	14.73%	57.24%	NA
All Indica	2759	16.70%	0.30%	17.62%	65.42%	NA
All Japonica	1512	41.70%	0.00%	10.38%	47.95%	NA
Aus	269	64.70%	0.00%	11.52%	23.79%	NA
Indica I	595	13.40%	0.00%	9.58%	76.97%	NA
Indica II	465	10.30%	0.20%	16.34%	73.12%	NA
Indica III	913	22.70%	0.70%	22.89%	53.78%	NA
Indica Intermediate	786	15.90%	0.10%	18.32%	65.65%	NA
Temperate Japonica	767	70.80%	0.00%	2.48%	26.73%	NA
Tropical Japonica	504	6.70%	0.00%	21.63%	71.63%	NA
Japonica Intermediate	241	22.00%	0.00%	12.03%	65.98%	NA
VI/Aromatic	96	30.20%	1.00%	9.38%	59.38%	NA
Intermediate	90	24.40%	1.10%	14.44%	60.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121848527	G -> A	LOC_Os11g37010.1	upstream_gene_variant ; 1708.0bp to feature; MODIFIER	silent_mutation	Average:7.256; most accessible tissue: Callus, score: 22.8	N	N	N	N
vg1121848527	G -> A	LOC_Os11g37000.1	downstream_gene_variant ; 4987.0bp to feature; MODIFIER	silent_mutation	Average:7.256; most accessible tissue: Callus, score: 22.8	N	N	N	N
vg1121848527	G -> A	LOC_Os11g37020.1	downstream_gene_variant ; 4845.0bp to feature; MODIFIER	silent_mutation	Average:7.256; most accessible tissue: Callus, score: 22.8	N	N	N	N
vg1121848527	G -> A	LOC_Os11g37000-LOC_Os11g37010	intergenic_region ; MODIFIER	silent_mutation	Average:7.256; most accessible tissue: Callus, score: 22.8	N	N	N	N
vg1121848527	G -> DEL	N	N	silent_mutation	Average:7.256; most accessible tissue: Callus, score: 22.8	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121848527	4.87E-06	NA	mr1902_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