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Detailed information for vg1120732145:

Variant ID: vg1120732145 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 20732145
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGTCAACGCGCTGGACTCCGTCAAGGGGCTAGAATCGGAGATGGCGTTGGACTCCGTCGAGGTGGCGTCGGACTCCGTCGAGGTGGCGCCGGACTCCGT[C/T]
GAGGTGGTGCAGTGTCCTCGCTGCGGCACATTCCATGCTGGCGGCGTCTTCGGAGAAGCATGCTTCCAAGCTTGCCGCCGTGCTCGCAGGTGTGCCCGTT

Reverse complement sequence

AACGGGCACACCTGCGAGCACGGCGGCAAGCTTGGAAGCATGCTTCTCCGAAGACGCCGCCAGCATGGAATGTGCCGCAGCGAGGACACTGCACCACCTC[G/A]
ACGGAGTCCGGCGCCACCTCGACGGAGTCCGACGCCACCTCGACGGAGTCCAACGCCATCTCCGATTCTAGCCCCTTGACGGAGTCCAGCGCGTTGACGA

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	91.90%	6.20%	1.42%	0.55%	NA
All Indica	2759	99.10%	0.20%	0.18%	0.51%	NA
All Japonica	1512	77.00%	18.60%	3.77%	0.66%	NA
Aus	269	98.10%	0.00%	1.12%	0.74%	NA
Indica I	595	99.30%	0.00%	0.67%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	99.30%	0.10%	0.00%	0.55%	NA
Indica Intermediate	786	98.50%	0.30%	0.13%	1.15%	NA
Temperate Japonica	767	92.70%	4.40%	2.48%	0.39%	NA
Tropical Japonica	504	63.70%	32.70%	3.57%	0.00%	NA
Japonica Intermediate	241	54.80%	34.00%	8.30%	2.90%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	5.60%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1120732145	C -> T	LOC_Os11g35370.1	synonymous_variant ; p.Val54Val; LOW	synonymous_codon	Average:62.242; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N
vg1120732145	C -> DEL	LOC_Os11g35370.1	N	frameshift_variant	Average:62.242; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120732145	2.37E-06	NA	mr1180_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