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Detailed information for vg1109788337:

Variant ID: vg1109788337 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9788337
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCATCTGCGGGTACGACGACTTGTCCCGGAGCAGCGCCCCGAGGTACGGCGGCACGGCGTCGTGGCGCCCCTCCACCACCTCCCTCGCCTCGATCTTGAC[T/G]
TTCTTTAGCACGGCGACGTCGTCGTGCGCCAGCACCAGCGCCAGCGCCAGGGACGACCTCACGTCGCCGCCGACGGCCGCCACCGTCGGGAAAGGCATGC

Reverse complement sequence

GCATGCCTTTCCCGACGGTGGCGGCCGTCGGCGGCGACGTGAGGTCGTCCCTGGCGCTGGCGCTGGTGCTGGCGCACGACGACGTCGCCGTGCTAAAGAA[A/C]
GTCAAGATCGAGGCGAGGGAGGTGGTGGAGGGGCGCCACGACGCCGTGCCGCCGTACCTCGGGGCGCTGCTCCGGGACAAGTCGTCGTACCCGCAGATGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.00%	6.00%	0.00%	0.00%	NA
All Indica	2759	92.90%	7.10%	0.00%	0.00%	NA
All Japonica	1512	98.90%	1.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	96.80%	3.20%	0.00%	0.00%	NA
Indica II	465	96.10%	3.90%	0.00%	0.00%	NA
Indica III	913	96.50%	3.50%	0.00%	0.00%	NA
Indica Intermediate	786	84.00%	16.00%	0.00%	0.00%	NA
Temperate Japonica	767	99.30%	0.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	3.30%	0.00%	0.00%	NA
VI/Aromatic	96	31.20%	68.80%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg1109788337	T -> G	LOC_Os11g17580.1	missense_variant ; p.Lys126Asn; MODERATE	nonsynonymous_codon ; K126N	Average:75.041; most accessible tissue: Zhenshan97 young leaf, score: 88.127	unknown	unknown	TOLERATED	0.35

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109788337	NA	4.11E-06	mr1100	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
vg1109788337	NA	6.84E-07	mr1723_2	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