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Detailed information for vg1124756486:

Variant ID: vg1124756486 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24756486
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTTCTCGAGCTCGATATCCTTCGCTCTCGTCCGGACCGCCGGCGCCGGCGACAATGTCCGTCTCCATGCGAGAGCCAAGATCAGCTTGCTCGACCTCGC[C/T]
GGCGAGCCGGTGGCACGGTACAGCCAACCCGTCGACAAGTGTTCCACCTCCAAGGCAAGCGATCCATGGGTTTGCAAGAGCTTCATCGAGAGGGATGAGC

Reverse complement sequence

GCTCATCCCTCTCGATGAAGCTCTTGCAAACCCATGGATCGCTTGCCTTGGAGGTGGAACACTTGTCGACGGGTTGGCTGTACCGTGCCACCGGCTCGCC[G/A]
GCGAGGTCGAGCAAGCTGATCTTGGCTCTCGCATGGAGACGGACATTGTCGCCGGCGCCGGCGGTCCGGACGAGAGCGAAGGATATCGAGCTCGAGAACT

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	97.30%	2.70%	0.00%	0.00%	NA
All Indica	2759	99.20%	0.80%	0.00%	0.00%	NA
All Japonica	1512	95.20%	4.80%	0.00%	0.00%	NA
Aus	269	90.30%	9.70%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	98.40%	1.60%	0.00%	0.00%	NA
Indica Intermediate	786	99.10%	0.90%	0.00%	0.00%	NA
Temperate Japonica	767	98.40%	1.60%	0.00%	0.00%	NA
Tropical Japonica	504	95.40%	4.60%	0.00%	0.00%	NA
Japonica Intermediate	241	84.20%	15.80%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg1124756486	C -> T	LOC_Os11g41300.1	synonymous_variant ; p.Ala107Ala; LOW	synonymous_codon	Average:75.941; most accessible tissue: Minghui63 flag leaf, score: 85.151	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124756486	NA	2.93E-06	mr1496	Jap_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