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Detailed information for vg1122346442:

Variant ID: vg1122346442 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22346442
Reference Allele: G	Alternative Allele: A,T
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

TTACCCATCGTTGGATATTTTAAATTTGAGGGGAGGTGTTCCGATGCGCGTGTGCGAAGGCCCGTGCATCGAAGCACAACGGTCGACAAAGGAGGTTTAA[G/A,T]
TGTTCAATAATTCAAGGAGGGTAATTGCAGCAATTAGGATTGGGGCCGGCAGGCTATCTCGCAAGCCGTGGCCGATTTACTTGTGTTAATCCTATTCATG

Reverse complement sequence

CATGAATAGGATTAACACAAGTAAATCGGCCACGGCTTGCGAGATAGCCTGCCGGCCCCAATCCTAATTGCTGCAATTACCCTCCTTGAATTATTGAACA[C/T,A]
TTAAACCTCCTTTGTCGACCGTTGTGCTTCGATGCACGGGCCTTCGCACACGCGCATCGGAACACCTCCCCTCAAATTTAAAATATCCAACGATGGGTAA

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	70.20%	8.20%	5.97%	15.53%	T: 0.04%
All Indica	2759	60.90%	13.50%	8.81%	16.82%	NA
All Japonica	1512	80.60%	0.60%	2.18%	16.53%	T: 0.13%
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	62.20%	2.70%	13.95%	21.18%	NA
Indica II	465	64.70%	14.20%	4.52%	16.56%	NA
Indica III	913	54.20%	20.40%	8.98%	16.43%	NA
Indica Intermediate	786	65.30%	13.40%	7.25%	14.12%	NA
Temperate Japonica	767	89.70%	0.40%	0.91%	8.87%	T: 0.13%
Tropical Japonica	504	75.60%	0.80%	3.37%	20.04%	T: 0.20%
Japonica Intermediate	241	61.80%	0.80%	3.73%	33.61%	NA
VI/Aromatic	96	95.80%	0.00%	2.08%	2.08%	NA
Intermediate	90	70.00%	5.60%	4.44%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122346442	G -> T	LOC_Os11g37774.1	upstream_gene_variant ; 4841.0bp to feature; MODIFIER	silent_mutation	Average:23.247; most accessible tissue: Minghui63 flag leaf, score: 53.617	N	N	N	N
vg1122346442	G -> T	LOC_Os11g37770-LOC_Os11g37774	intergenic_region ; MODIFIER	silent_mutation	Average:23.247; most accessible tissue: Minghui63 flag leaf, score: 53.617	N	N	N	N
vg1122346442	G -> A	LOC_Os11g37774.1	upstream_gene_variant ; 4841.0bp to feature; MODIFIER	silent_mutation	Average:23.247; most accessible tissue: Minghui63 flag leaf, score: 53.617	N	N	N	N
vg1122346442	G -> A	LOC_Os11g37770-LOC_Os11g37774	intergenic_region ; MODIFIER	silent_mutation	Average:23.247; most accessible tissue: Minghui63 flag leaf, score: 53.617	N	N	N	N
vg1122346442	G -> DEL	N	N	silent_mutation	Average:23.247; most accessible tissue: Minghui63 flag leaf, score: 53.617	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122346442	4.95E-06	NA	mr1015_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