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Detailed information for vg1109788343:

Variant ID: vg1109788343 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9788343
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCGGGTACGACGACTTGTCCCGGAGCAGCGCCCCGAGGTACGGCGGCACGGCGTCGTGGCGCCCCTCCACCACCTCCCTCGCCTCGATCTTGACTTTCTT[T/C]
AGCACGGCGACGTCGTCGTGCGCCAGCACCAGCGCCAGCGCCAGGGACGACCTCACGTCGCCGCCGACGGCCGCCACCGTCGGGAAAGGCATGCCCAGCA

Reverse complement sequence

TGCTGGGCATGCCTTTCCCGACGGTGGCGGCCGTCGGCGGCGACGTGAGGTCGTCCCTGGCGCTGGCGCTGGTGCTGGCGCACGACGACGTCGCCGTGCT[A/G]
AAGAAAGTCAAGATCGAGGCGAGGGAGGTGGTGGAGGGGCGCCACGACGCCGTGCCGCCGTACCTCGGGGCGCTGCTCCGGGACAAGTCGTCGTACCCGC

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	62.50%	37.50%	0.02%	0.00%	NA
All Indica	2759	92.50%	7.40%	0.04%	0.00%	NA
All Japonica	1512	2.70%	97.30%	0.00%	0.00%	NA
Aus	269	83.60%	16.40%	0.00%	0.00%	NA
Indica I	595	88.70%	11.30%	0.00%	0.00%	NA
Indica II	465	91.40%	8.60%	0.00%	0.00%	NA
Indica III	913	97.40%	2.60%	0.00%	0.00%	NA
Indica Intermediate	786	90.50%	9.40%	0.13%	0.00%	NA
Temperate Japonica	767	1.40%	98.60%	0.00%	0.00%	NA
Tropical Japonica	504	3.60%	96.40%	0.00%	0.00%	NA
Japonica Intermediate	241	5.00%	95.00%	0.00%	0.00%	NA
VI/Aromatic	96	79.20%	20.80%	0.00%	0.00%	NA
Intermediate	90	63.30%	36.70%	0.00%	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
vg1109788343	T -> C	LOC_Os11g17580.1	synonymous_variant ; p.Leu124Leu; LOW	synonymous_codon	Average:74.873; most accessible tissue: Zhenshan97 young leaf, score: 87.859	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109788343	NA	5.26E-09	mr1595	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