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Detailed information for vg1111530123:

Variant ID: vg1111530123 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 11530123
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTGATGTAAATCACATGTGAGACACACACAACCAAATTTAAACGAACAAACTAACACAACAATCTAAGACAACGGCTTAACAAGGCACTCTAGGTCTTC[C/T]
GGGCATCGAAGTTGATTGAAGGCTCGTTCGGCTCGTCTCCATCATCTTGAGTAGCACCCCACTCAACCTTTGAATGGGTGCGCTTCGATTCTTCTCCTTC

Reverse complement sequence

GAAGGAGAAGAATCGAAGCGCACCCATTCAAAGGTTGAGTGGGGTGCTACTCAAGATGATGGAGACGAGCCGAACGAGCCTTCAATCAACTTCGATGCCC[G/A]
GAAGACCTAGAGTGCCTTGTTAAGCCGTTGTCTTAGATTGTTGTGTTAGTTTGTTCGTTTAAATTTGGTTGTGTGTGTCTCACATGTGATTTACATCAGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	45.10%	0.40%	27.00%	27.44%	NA
All Indica	2759	18.60%	0.10%	40.59%	40.74%	NA
All Japonica	1512	95.00%	1.10%	1.39%	2.45%	NA
Aus	269	20.40%	0.00%	39.78%	39.78%	NA
Indica I	595	13.60%	0.00%	31.09%	55.29%	NA
Indica II	465	10.10%	0.00%	45.38%	44.52%	NA
Indica III	913	26.80%	0.10%	46.11%	26.94%	NA
Indica Intermediate	786	17.80%	0.10%	38.55%	43.51%	NA
Temperate Japonica	767	98.00%	0.10%	0.52%	1.30%	NA
Tropical Japonica	504	89.70%	2.80%	2.58%	4.96%	NA
Japonica Intermediate	241	96.70%	0.80%	1.66%	0.83%	NA
VI/Aromatic	96	90.60%	0.00%	7.29%	2.08%	NA
Intermediate	90	45.60%	1.10%	23.33%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1111530123	C -> T	LOC_Os11g20030.1	intron_variant ; MODIFIER	silent_mutation	Average:7.054; most accessible tissue: Minghui63 flower, score: 11.852	N	N	N	N
vg1111530123	C -> DEL	N	N	silent_mutation	Average:7.054; most accessible tissue: Minghui63 flower, score: 11.852	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1111530123	NA	6.62E-08	mr1044	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
vg1111530123	4.05E-06	7.34E-08	mr1044	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
vg1111530123	NA	6.29E-06	mr1842	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