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Detailed information for vg1128769378:

Variant ID: vg1128769378 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 28769378
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATCTAAACCCTGGATTTTGCTTAGTGGTAGCTTGTTGTCGAAACAAGATTTCGGCAATACTAAAATGGGTGGCTATCAAGCTAGAAAAGTCGATGGGTT[T/C]
GGAAACAAGGAATTTTATATAGGTTCAGGCTTTCTTAATCAAGAAGTAATACCCTACTTGTAGTGTGGATTGGAAACATATTGAACCCAAAATATGCAAG

Reverse complement sequence

CTTGCATATTTTGGGTTCAATATGTTTCCAATCCACACTACAAGTAGGGTATTACTTCTTGATTAAGAAAGCCTGAACCTATATAAAATTCCTTGTTTCC[A/G]
AACCCATCGACTTTTCTAGCTTGATAGCCACCCATTTTAGTATTGCCGAAATCTTGTTTCGACAACAAGCTACCACTAAGCAAAATCCAGGGTTTAGATA

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	72.90%	23.40%	1.35%	2.35%	NA
All Indica	2759	79.00%	18.50%	0.76%	1.74%	NA
All Japonica	1512	57.50%	37.00%	1.85%	3.64%	NA
Aus	269	94.10%	4.80%	0.74%	0.37%	NA
Indica I	595	75.10%	23.40%	0.50%	1.01%	NA
Indica II	465	82.40%	12.50%	0.22%	4.95%	NA
Indica III	913	81.40%	17.10%	0.66%	0.88%	NA
Indica Intermediate	786	77.20%	20.00%	1.40%	1.40%	NA
Temperate Japonica	767	72.90%	18.40%	3.00%	5.74%	NA
Tropical Japonica	504	29.80%	68.10%	0.40%	1.79%	NA
Japonica Intermediate	241	66.40%	31.50%	1.24%	0.83%	NA
VI/Aromatic	96	79.20%	7.30%	12.50%	1.04%	NA
Intermediate	90	73.30%	18.90%	1.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1128769378	T -> DEL	N	N	silent_mutation	Average:44.817; most accessible tissue: Zhenshan97 root, score: 85.305	N	N	N	N
vg1128769378	T -> C	LOC_Os11g47630.1	upstream_gene_variant ; 2441.0bp to feature; MODIFIER	silent_mutation	Average:44.817; most accessible tissue: Zhenshan97 root, score: 85.305	N	N	N	N
vg1128769378	T -> C	LOC_Os11g47640.1	upstream_gene_variant ; 226.0bp to feature; MODIFIER	silent_mutation	Average:44.817; most accessible tissue: Zhenshan97 root, score: 85.305	N	N	N	N
vg1128769378	T -> C	LOC_Os11g47630-LOC_Os11g47640	intergenic_region ; MODIFIER	silent_mutation	Average:44.817; most accessible tissue: Zhenshan97 root, score: 85.305	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1128769378	2.46E-06	2.46E-06	mr1168	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