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Detailed information for vg1105927518:

Variant ID: vg1105927518 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5927518
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTGCTCATAGGGGGTGCTCAAGATATGCCGACTCAGTCTTCCGGAGGTGTTCATAGGGTGGTGACTTCGTCAATCTCAAGATATGCTCAATATATGCTG[G/A]
CTCAGTCTTCCGGAGGTGCTCATAGGGGGTTCTCAAGATATGCCGGCTCAGTCTTTCGGAGGTGCTCATAGGGTGGTGACTTCGTCAATCTCAAGATATG

Reverse complement sequence

CATATCTTGAGATTGACGAAGTCACCACCCTATGAGCACCTCCGAAAGACTGAGCCGGCATATCTTGAGAACCCCCTATGAGCACCTCCGGAAGACTGAG[C/T]
CAGCATATATTGAGCATATCTTGAGATTGACGAAGTCACCACCCTATGAACACCTCCGGAAGACTGAGTCGGCATATCTTGAGCACCCCCTATGAGCACC

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	36.30%	3.30%	0.80%	59.63%	NA
All Indica	2759	16.70%	1.30%	1.01%	80.97%	NA
All Japonica	1512	72.90%	7.60%	0.33%	19.18%	NA
Aus	269	8.60%	0.00%	0.37%	91.08%	NA
Indica I	595	7.90%	0.30%	0.50%	91.26%	NA
Indica II	465	7.70%	0.00%	2.15%	90.11%	NA
Indica III	913	23.30%	2.10%	0.99%	73.60%	NA
Indica Intermediate	786	21.00%	1.90%	0.76%	76.34%	NA
Temperate Japonica	767	66.10%	2.30%	0.52%	31.03%	NA
Tropical Japonica	504	81.20%	14.70%	0.20%	3.97%	NA
Japonica Intermediate	241	77.20%	9.50%	0.00%	13.28%	NA
VI/Aromatic	96	88.50%	0.00%	2.08%	9.38%	NA
Intermediate	90	48.90%	4.40%	2.22%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1105927518	G -> A	LOC_Os11g10780.1	upstream_gene_variant ; 3740.0bp to feature; MODIFIER	silent_mutation	Average:20.976; most accessible tissue: Callus, score: 34.728	N	N	N	N
vg1105927518	G -> A	LOC_Os11g10780-LOC_Os11g10790	intergenic_region ; MODIFIER	silent_mutation	Average:20.976; most accessible tissue: Callus, score: 34.728	N	N	N	N
vg1105927518	G -> DEL	N	N	silent_mutation	Average:20.976; most accessible tissue: Callus, score: 34.728	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105927518	NA	1.42E-06	mr1236	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
vg1105927518	1.02E-06	1.76E-11	mr1248	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