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Detailed information for vg1209716053:

Variant ID: vg1209716053 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 9716053
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAATACTTTTGGCTCAGAGTTCCCCTCAGTTGAAATCCAGCACCCCCAACTACGCATGGCTTGCTCTTGTTCGGTTGGGGTTTGAGGAAGAAGATATAGC[A/G]
GAATAGGGCAAAATGTGGCCTGACGCCCATAAAAGCTTCGCAGGCATGTATGAAGTTGGCAATATGAACTATGGAATTCGGGTTTAGGTGATGCAAACTA

Reverse complement sequence

TAGTTTGCATCACCTAAACCCGAATTCCATAGTTCATATTGCCAACTTCATACATGCCTGCGAAGCTTTTATGGGCGTCAGGCCACATTTTGCCCTATTC[T/C]
GCTATATCTTCTTCCTCAAACCCCAACCGAACAAGAGCAAGCCATGCGTAGTTGGGGGTGCTGGATTTCAACTGAGGGGAACTCTGAGCCAAAAGTATTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.40%	2.70%	1.21%	28.67%	NA
All Indica	2759	49.80%	1.70%	2.03%	46.50%	NA
All Japonica	1512	95.80%	1.50%	0.00%	2.71%	NA
Aus	269	81.40%	18.20%	0.00%	0.37%	NA
Indica I	595	66.70%	0.20%	0.84%	32.27%	NA
Indica II	465	55.30%	0.00%	1.08%	43.66%	NA
Indica III	913	33.50%	3.40%	3.18%	59.91%	NA
Indica Intermediate	786	52.50%	1.90%	2.16%	43.38%	NA
Temperate Japonica	767	92.70%	2.70%	0.00%	4.56%	NA
Tropical Japonica	504	98.60%	0.20%	0.00%	1.19%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	72.90%	7.30%	1.04%	18.75%	NA
Intermediate	90	83.30%	3.30%	0.00%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1209716053	A -> DEL	LOC_Os12g16960.1	N	frameshift_variant	Average:53.471; most accessible tissue: Minghui63 flag leaf, score: 79.676	N	N	N	N
vg1209716053	A -> G	LOC_Os12g16960.1	missense_variant ; p.Cys117Arg; MODERATE	nonsynonymous_codon ; C117R	Average:53.471; most accessible tissue: Minghui63 flag leaf, score: 79.676	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209716053	4.06E-06	4.06E-06	mr1355	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