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Detailed information for vg1122165203:

Variant ID: vg1122165203 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22165203
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

AAATTTCTCAAATTGATCATCATATAACCGCATGAATATGGATTTCATCGAAATACAATTAATGCGACATGGGAGAATGTGTGCGTGCTAGGATGTAATT[G/A]
GCATGGTGTTGTAATCGATGCATGCATTGTGGGAGAATGTGTGCATGATGTATTGATTGATGCGATTTAAATTATCCTTGGTCTTGGTGCATAAACATAT

Reverse complement sequence

ATATGTTTATGCACCAAGACCAAGGATAATTTAAATCGCATCAATCAATACATCATGCACACATTCTCCCACAATGCATGCATCGATTACAACACCATGC[C/T]
AATTACATCCTAGCACGCACACATTCTCCCATGTCGCATTAATTGTATTTCGATGAAATCCATATTCATGCGGTTATATGATGATCAATTTGAGAAATTT

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	70.40%	28.60%	0.13%	0.85%	NA
All Indica	2759	70.20%	29.60%	0.18%	0.00%	NA
All Japonica	1512	73.10%	24.30%	0.07%	2.51%	NA
Aus	269	46.80%	52.40%	0.00%	0.74%	NA
Indica I	595	46.90%	52.80%	0.34%	0.00%	NA
Indica II	465	70.30%	29.20%	0.43%	0.00%	NA
Indica III	913	82.10%	17.90%	0.00%	0.00%	NA
Indica Intermediate	786	74.00%	25.80%	0.13%	0.00%	NA
Temperate Japonica	767	90.20%	8.70%	0.00%	1.04%	NA
Tropical Japonica	504	57.10%	39.90%	0.00%	2.98%	NA
Japonica Intermediate	241	52.30%	41.10%	0.41%	6.22%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	74.40%	25.60%	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
vg1122165203	G -> A	LOC_Os11g37540.1	intron_variant ; MODIFIER	silent_mutation	Average:41.627; most accessible tissue: Zhenshan97 root, score: 58.674	N	N	N	N
vg1122165203	G -> DEL	N	N	silent_mutation	Average:41.627; most accessible tissue: Zhenshan97 root, score: 58.674	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122165203	NA	3.85E-07	mr1222_2	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
vg1122165203	NA	9.93E-06	mr1359_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
vg1122165203	1.79E-06	NA	mr1793_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