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Detailed information for vg1118883359:

Variant ID: vg1118883359 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 18883359
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACATTTAAGATCCTTCAAAGAAAAGACATTCATCCAGTGGCACTATCAGACATAAAATATACTCCCTCCGTTTTAGGTTATAAGACTTTCTAGTAGTACC[C/T]
ATATTCATATAGATATTAATGAATCCAGACACACATATATGTTTAGATTCATTAACATCATTAACATATGTTTTTAATATGGACATTGCTATGAAACGGA

Reverse complement sequence

TCCGTTTCATAGCAATGTCCATATTAAAAACATATGTTAATGATGTTAATGAATCTAAACATATATGTGTGTCTGGATTCATTAATATCTATATGAATAT[G/A]
GGTACTACTAGAAAGTCTTATAACCTAAAACGGAGGGAGTATATTTTATGTCTGATAGTGCCACTGGATGAATGTCTTTTCTTTGAAGGATCTTAAATGT

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	97.60%	2.30%	0.08%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.04%	0.00%	NA
All Japonica	1512	93.10%	6.70%	0.20%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.70%	0.20%	0.11%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	97.50%	2.50%	0.00%	0.00%	NA
Tropical Japonica	504	83.70%	15.70%	0.60%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	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
vg1118883359	C -> T	LOC_Os11g32040.1	downstream_gene_variant ; 125.0bp to feature; MODIFIER	silent_mutation	Average:47.734; most accessible tissue: Zhenshan97 young leaf, score: 66.83	N	N	N	N
vg1118883359	C -> T	LOC_Os11g32050.1	downstream_gene_variant ; 2510.0bp to feature; MODIFIER	silent_mutation	Average:47.734; most accessible tissue: Zhenshan97 young leaf, score: 66.83	N	N	N	N
vg1118883359	C -> T	LOC_Os11g32030-LOC_Os11g32040	intergenic_region ; MODIFIER	silent_mutation	Average:47.734; most accessible tissue: Zhenshan97 young leaf, score: 66.83	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1118883359	2.92E-07	2.92E-07	mr1344	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
vg1118883359	NA	6.93E-06	mr1607	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