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Detailed information for vg1115774318:

Variant ID: vg1115774318 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 15774318
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTCAGCTTGGTGGGACAATCACATGGCCACCCGCCCACCAGGTACTGAAGTCACTTGGGCAGAGTTCTGCCGTAGCTTCAGGAAGGCGCAGGTGCCAGA[C/T]
GGGGTCGTGGCACAAGAGAAGAGGGAATTTCGGGCACTCCATCAGGGCAACAGGACTATGACGGAGTACCTCCATGAGTTCAATCGCCTCGCGCGATATG

Reverse complement sequence

CATATCGCGCGAGGCGATTGAACTCATGGAGGTACTCCGTCATAGTCCTGTTGCCCTGATGGAGTGCCCGAAATTCCCTCTTCTCTTGTGCCACGACCCC[G/A]
TCTGGCACCTGCGCCTTCCTGAAGCTACGGCAGAACTCTGCCCAAGTGACTTCAGTACCTGGTGGGCGGGTGGCCATGTGATTGTCCCACCAAGCTGACG

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	65.00%	0.10%	8.34%	26.58%	NA
All Indica	2759	43.50%	0.20%	13.48%	42.77%	NA
All Japonica	1512	98.30%	0.00%	0.20%	1.46%	NA
Aus	269	84.00%	0.00%	4.46%	11.52%	NA
Indica I	595	27.10%	0.20%	9.92%	62.86%	NA
Indica II	465	47.50%	0.40%	8.60%	43.44%	NA
Indica III	913	50.90%	0.10%	19.06%	29.90%	NA
Indica Intermediate	786	45.00%	0.30%	12.60%	42.11%	NA
Temperate Japonica	767	98.40%	0.00%	0.13%	1.43%	NA
Tropical Japonica	504	97.80%	0.00%	0.40%	1.79%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	68.90%	0.00%	7.78%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1115774318	C -> T	LOC_Os11g27410.1	synonymous_variant ; p.Asp390Asp; LOW	synonymous_codon	Average:11.671; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N
vg1115774318	C -> DEL	LOC_Os11g27410.1	N	frameshift_variant	Average:11.671; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1115774318	NA	9.66E-06	mr1391_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
vg1115774318	7.73E-07	NA	mr1612_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