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Detailed information for vg1109924210:

Variant ID: vg1109924210 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9924210
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGAGAGATTAAAACCTAAACCAAGGGAACAGAGATAGAAGTCTCACCGAACCAAACGATTGGAGAGGGAGAGATGACGACGGCGACCCGGCGGCAACACA[C/T]
GGAGACGACGACGATGCTAGACAAACAACGGATTAGATTGAATTTGATCTAGGGTTTAGGTAGACGTGGCAATGATAAGACAGCCAAGCGAGATCATCGG

Reverse complement sequence

CCGATGATCTCGCTTGGCTGTCTTATCATTGCCACGTCTACCTAAACCCTAGATCAAATTCAATCTAATCCGTTGTTTGTCTAGCATCGTCGTCGTCTCC[G/A]
TGTGTTGCCGCCGGGTCGCCGTCGTCATCTCTCCCTCTCCAATCGTTTGGTTCGGTGAGACTTCTATCTCTGTTCCCTTGGTTTAGGTTTTAATCTCTCG

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	41.90%	0.80%	1.65%	55.69%	NA
All Indica	2759	15.40%	1.20%	2.54%	80.79%	NA
All Japonica	1512	95.80%	0.00%	0.07%	4.17%	NA
Aus	269	17.10%	0.40%	1.49%	81.04%	NA
Indica I	595	23.20%	0.20%	1.34%	75.29%	NA
Indica II	465	11.40%	0.60%	1.94%	86.02%	NA
Indica III	913	5.30%	2.30%	3.94%	88.50%	NA
Indica Intermediate	786	23.80%	1.10%	2.16%	72.90%	NA
Temperate Japonica	767	97.00%	0.00%	0.00%	3.00%	NA
Tropical Japonica	504	94.20%	0.00%	0.20%	5.56%	NA
Japonica Intermediate	241	95.00%	0.00%	0.00%	4.98%	NA
VI/Aromatic	96	19.80%	1.00%	0.00%	79.17%	NA
Intermediate	90	43.30%	2.20%	3.33%	51.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109924210	C -> T	LOC_Os11g17760.1	upstream_gene_variant ; 228.0bp to feature; MODIFIER	silent_mutation	Average:17.841; most accessible tissue: Callus, score: 55.633	N	N	N	N
vg1109924210	C -> T	LOC_Os11g17740-LOC_Os11g17760	intergenic_region ; MODIFIER	silent_mutation	Average:17.841; most accessible tissue: Callus, score: 55.633	N	N	N	N
vg1109924210	C -> DEL	N	N	silent_mutation	Average:17.841; most accessible tissue: Callus, score: 55.633	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109924210	5.67E-07	NA	mr1855	Ind_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