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Detailed information for vg1120967952:

Variant ID: vg1120967952 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 20967952
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTAGTTACAGATTCTGAAAAATAAACTAAGAAACCAGAAGCTGGAGAAACTGGGTTTCAGAGTTTTTCCAGATTTTTAAAAGCTGGCTACCAAATAGCT[G/A]
CTTCTCAGAATCTAAAGCTCCCCTAAACAGAGCCAAATAACGCAGCCATAGCACAGCTGCCAAGTTCTTGCTGCTCATGGCAACCCTGGCCTGCTTCTCT

Reverse complement sequence

AGAGAAGCAGGCCAGGGTTGCCATGAGCAGCAAGAACTTGGCAGCTGTGCTATGGCTGCGTTATTTGGCTCTGTTTAGGGGAGCTTTAGATTCTGAGAAG[C/T]
AGCTATTTGGTAGCCAGCTTTTAAAAATCTGGAAAAACTCTGAAACCCAGTTTCTCCAGCTTCTGGTTTCTTAGTTTATTTTTCAGAATCTGTAACTACA

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	86.50%	12.40%	0.02%	1.10%	NA
All Indica	2759	85.60%	13.10%	0.04%	1.27%	NA
All Japonica	1512	95.40%	3.70%	0.00%	0.93%	NA
Aus	269	44.20%	55.40%	0.00%	0.37%	NA
Indica I	595	96.30%	3.70%	0.00%	0.00%	NA
Indica II	465	81.70%	15.50%	0.00%	2.80%	NA
Indica III	913	81.30%	17.60%	0.11%	0.99%	NA
Indica Intermediate	786	84.70%	13.60%	0.00%	1.65%	NA
Temperate Japonica	767	99.20%	0.70%	0.00%	0.13%	NA
Tropical Japonica	504	88.90%	8.50%	0.00%	2.58%	NA
Japonica Intermediate	241	96.70%	3.30%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	80.00%	17.80%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1120967952	G -> A	LOC_Os11g35720-LOC_Os11g35730	intergenic_region ; MODIFIER	silent_mutation	Average:72.652; most accessible tissue: Minghui63 panicle, score: 86.85	N	N	N	N
vg1120967952	G -> DEL	N	N	silent_mutation	Average:72.652; most accessible tissue: Minghui63 panicle, score: 86.85	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120967952	9.50E-06	NA	mr1218_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
vg1120967952	NA	3.99E-06	mr1318_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
vg1120967952	6.59E-06	NA	mr1422_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
vg1120967952	NA	8.66E-07	mr1498_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
vg1120967952	NA	1.74E-06	mr1511_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
vg1120967952	3.56E-06	1.95E-14	mr1583_2	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
vg1120967952	NA	9.25E-07	mr1583_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
vg1120967952	NA	1.30E-06	mr1638_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
vg1120967952	NA	3.33E-06	mr1729_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
vg1120967952	NA	2.61E-08	mr1740_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
vg1120967952	NA	2.81E-10	mr1741_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
vg1120967952	NA	9.35E-06	mr1887_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
vg1120967952	NA	3.45E-07	mr1951_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