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Detailed information for vg1126088739:

Variant ID: vg1126088739 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26088739
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAACTGTGGTTATATCCTTCCATTCACGGGATCTTGAAGGAAACGGTATGTTGACGCCGTTGATCCATAGCTCCTTCAAGTTTTGAAGATTTTCGATCCC[T/C]
TTGATGTTGTTTACCGTGATCCCCATCAGCGTTGTCATCGTGTCGAAGTTCCAGACAATCTTCTCCAGCTTGGGAGCTGCATCTTCTTCGAAGACAAGTT

Reverse complement sequence

AACTTGTCTTCGAAGAAGATGCAGCTCCCAAGCTGGAGAAGATTGTCTGGAACTTCGACACGATGACAACGCTGATGGGGATCACGGTAAACAACATCAA[A/G]
GGGATCGAAAATCTTCAAAACTTGAAGGAGCTATGGATCAACGGCGTCAACATACCGTTTCCTTCAAGATCCCGTGAATGGAAGGATATAACCACAGTTC

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	94.40%	5.60%	0.06%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	82.50%	17.30%	0.20%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	68.40%	31.30%	0.26%	0.00%	NA
Tropical Japonica	504	98.80%	1.00%	0.20%	0.00%	NA
Japonica Intermediate	241	93.40%	6.60%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg1126088739	T -> C	LOC_Os11g43250.1	synonymous_variant ; p.Lys795Lys; LOW	synonymous_codon	Average:50.327; most accessible tissue: Zhenshan97 young leaf, score: 73.923	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126088739	NA	2.71E-06	mr1062_2	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
vg1126088739	3.16E-06	3.16E-06	mr1173_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