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Detailed information for vg1109865369:

Variant ID: vg1109865369 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9865369
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, A: 0.08, others allele: 0.00, population size: 38. )

Flanking Sequence (100 bp) in Reference Genome:

GGGCGGTTATGGCCGCCGAAGAGGGAGCAGAGCCTTCGGCGCCCATCGCCGAAGATGGAGGAGCGCCATCTGCTTCCGCACCTGCGCCATCACTACCGCC[A/T]
TCGGCTCCTGGCCCCTCCACACAGGTGCCGAACGCGGCTGACATGGCGAAGGCGGCTGCGGTGGCAAGGGCACTCCAGACCAAGGCAGAGATCCTTTCGA

Reverse complement sequence

TCGAAAGGATCTCTGCCTTGGTCTGGAGTGCCCTTGCCACCGCAGCCGCCTTCGCCATGTCAGCCGCGTTCGGCACCTGTGTGGAGGGGCCAGGAGCCGA[T/A]
GGCGGTAGTGATGGCGCAGGTGCGGAAGCAGATGGCGCTCCTCCATCTTCGGCGATGGGCGCCGAAGGCTCTGCTCCCTCTTCGGCGGCCATAACCGCCC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	26.60%	11.20%	10.24%	51.93%	NA
All Indica	2759	12.70%	0.90%	11.05%	75.39%	NA
All Japonica	1512	56.00%	32.30%	8.47%	3.17%	NA
Aus	269	10.00%	0.70%	11.15%	78.07%	NA
Indica I	595	9.90%	0.70%	24.54%	64.87%	NA
Indica II	465	5.60%	1.10%	10.11%	83.23%	NA
Indica III	913	14.00%	0.10%	2.63%	83.24%	NA
Indica Intermediate	786	17.40%	1.80%	11.20%	69.59%	NA
Temperate Japonica	767	29.60%	56.80%	10.95%	2.61%	NA
Tropical Japonica	504	89.50%	3.20%	3.97%	3.37%	NA
Japonica Intermediate	241	70.10%	15.40%	9.96%	4.56%	NA
VI/Aromatic	96	15.60%	1.00%	7.29%	76.04%	NA
Intermediate	90	22.20%	14.40%	15.56%	47.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109865369	A -> T	LOC_Os11g17670.1	synonymous_variant ; p.Pro208Pro; LOW	synonymous_codon	Average:14.176; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg1109865369	A -> DEL	LOC_Os11g17670.1	N	frameshift_variant	Average:14.176; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109865369	3.16E-06	3.16E-06	mr1477_2	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
vg1109865369	NA	4.63E-06	mr1902_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
vg1109865369	NA	1.12E-06	mr1957_2	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