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Detailed information for vg1105432446:

Variant ID: vg1105432446 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5432446
Reference Allele: C	Alternative Allele: A,T
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCATATCACCAAATCCGCATCACAAATCTTAAAGTTACACACAAATCAAATACATCATAGATCTAAAAAATTACACACAAATCAAATACATCACAGATC[C/A,T]
ATACAATAAATCACAAATTTATACATATCAGGGAATCACAAATTATAAAAAAAAACACAAAGCCGCTCGCAGCCGCCCGGCGCCACCGCCCGCCACGGCC

Reverse complement sequence

GGCCGTGGCGGGCGGTGGCGCCGGGCGGCTGCGAGCGGCTTTGTGTTTTTTTTTATAATTTGTGATTCCCTGATATGTATAAATTTGTGATTTATTGTAT[G/T,A]
GATCTGTGATGTATTTGATTTGTGTGTAATTTTTTAGATCTATGATGTATTTGATTTGTGTGTAACTTTAAGATTTGTGATGCGGATTTGGTGATATGAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.60%	11.30%	2.14%	0.00%	NA
All Indica	2759	79.60%	18.30%	2.14%	0.00%	NA
All Japonica	1512	96.20%	1.00%	2.78%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	84.70%	15.10%	0.17%	0.00%	NA
Indica II	465	91.20%	7.30%	1.51%	0.00%	NA
Indica III	913	73.10%	23.40%	3.50%	0.00%	NA
Indica Intermediate	786	76.30%	21.20%	2.42%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	88.90%	3.00%	8.13%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	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
vg1105432446	C -> T	LOC_Os11g10080.1	upstream_gene_variant ; 4439.0bp to feature; MODIFIER	N	Average:60.518; most accessible tissue: Minghui63 young leaf, score: 80.883	N	N	N	N
vg1105432446	C -> T	LOC_Os11g10070-LOC_Os11g10080	intergenic_region ; MODIFIER	N	Average:60.518; most accessible tissue: Minghui63 young leaf, score: 80.883	N	N	N	N
vg1105432446	C -> A	LOC_Os11g10080.1	upstream_gene_variant ; 4439.0bp to feature; MODIFIER	silent_mutation	Average:60.518; most accessible tissue: Minghui63 young leaf, score: 80.883	N	N	N	N
vg1105432446	C -> A	LOC_Os11g10070-LOC_Os11g10080	intergenic_region ; MODIFIER	silent_mutation	Average:60.518; most accessible tissue: Minghui63 young leaf, score: 80.883	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105432446	4.48E-06	4.48E-06	mr1281_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