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Detailed information for vg1127555232:

Variant ID: vg1127555232 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27555232
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTGCTCGTAGCTCATGTAGTCTGCCACCCATTTGGTACTCTTGGAGAGCATGGAGCTTCTACTGGCTAGCTTGAACGACGCGACCCGTGTGCCGGATTT[C/T]
AATATGACTATGCAGTATATGACCCATAGAATGTACTGGAAATCCGAGCCACCAGAGGAAACCACCAGCCAACCCACCCAGAAAGACTCGATGAGCTGCT

Reverse complement sequence

AGCAGCTCATCGAGTCTTTCTGGGTGGGTTGGCTGGTGGTTTCCTCTGGTGGCTCGGATTTCCAGTACATTCTATGGGTCATATACTGCATAGTCATATT[G/A]
AAATCCGGCACACGGGTCGCGTCGTTCAAGCTAGCCAGTAGAAGCTCCATGCTCTCCAAGAGTACCAAATGGGTGGCAGACTACATGAGCTACGAGCACC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	31.20%	15.70%	0.44%	52.58%	NA
All Indica	2759	44.30%	3.10%	0.33%	52.23%	NA
All Japonica	1512	8.90%	39.90%	0.73%	50.40%	NA
Aus	269	6.30%	11.50%	0.37%	81.78%	NA
Indica I	595	63.90%	4.00%	0.00%	32.10%	NA
Indica II	465	82.40%	1.70%	0.22%	15.70%	NA
Indica III	913	12.80%	1.60%	0.55%	84.99%	NA
Indica Intermediate	786	43.60%	5.00%	0.38%	51.02%	NA
Temperate Japonica	767	10.00%	53.10%	1.30%	35.59%	NA
Tropical Japonica	504	3.20%	25.00%	0.20%	71.63%	NA
Japonica Intermediate	241	17.40%	29.50%	0.00%	53.11%	NA
VI/Aromatic	96	66.70%	0.00%	0.00%	33.33%	NA
Intermediate	90	41.10%	25.60%	0.00%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127555232	C -> T	LOC_Os11g45510.1	synonymous_variant ; p.Leu98Leu; LOW	synonymous_codon	Average:12.279; most accessible tissue: Callus, score: 81.317	N	N	N	N
vg1127555232	C -> DEL	LOC_Os11g45510.1	N	frameshift_variant	Average:12.279; most accessible tissue: Callus, score: 81.317	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127555232	1.36E-06	2.09E-07	mr1803	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