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Detailed information for vg1127976664:

Variant ID: vg1127976664 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27976664
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACAGTTCATTGAATTTTCAACTTCACATGTTAAATGTATTATTTCTATCAGGTTATTGATACGTGTATACTATTATTATATGGATGGCATTAGCAACGA[G/T]
GCGGTTCATTAAAATTATCGAAATAGTACATTGAGCATGTGAAGTTTGAATCTTATGAGCACATATATTTTACTTGCAGGGTCTTTGTAAACAATCTTGT

Reverse complement sequence

ACAAGATTGTTTACAAAGACCCTGCAAGTAAAATATATGTGCTCATAAGATTCAAACTTCACATGCTCAATGTACTATTTCGATAATTTTAATGAACCGC[C/A]
TCGTTGCTAATGCCATCCATATAATAATAGTATACACGTATCAATAACCTGATAGAAATAATACATTTAACATGTGAAGTTGAAAATTCAATGAACTGTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.60%	3.60%	1.10%	48.73%	NA
All Indica	2759	46.20%	3.70%	0.87%	49.18%	NA
All Japonica	1512	45.80%	3.50%	1.59%	49.14%	NA
Aus	269	58.70%	0.40%	0.74%	40.15%	NA
Indica I	595	59.70%	0.00%	0.34%	40.00%	NA
Indica II	465	19.10%	0.00%	1.08%	79.78%	NA
Indica III	913	52.90%	10.50%	1.10%	35.49%	NA
Indica Intermediate	786	44.40%	0.80%	0.89%	53.94%	NA
Temperate Japonica	767	38.60%	6.10%	1.30%	53.98%	NA
Tropical Japonica	504	56.90%	0.00%	1.98%	41.07%	NA
Japonica Intermediate	241	45.20%	2.50%	1.66%	50.62%	NA
VI/Aromatic	96	21.90%	12.50%	2.08%	63.54%	NA
Intermediate	90	58.90%	3.30%	0.00%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127976664	G -> T	LOC_Os11g46190.1	upstream_gene_variant ; 1829.0bp to feature; MODIFIER	silent_mutation	Average:30.267; most accessible tissue: Zhenshan97 root, score: 79.962	N	N	N	N
vg1127976664	G -> T	LOC_Os11g46200.1	downstream_gene_variant ; 1704.0bp to feature; MODIFIER	silent_mutation	Average:30.267; most accessible tissue: Zhenshan97 root, score: 79.962	N	N	N	N
vg1127976664	G -> T	LOC_Os11g46190-LOC_Os11g46200	intergenic_region ; MODIFIER	silent_mutation	Average:30.267; most accessible tissue: Zhenshan97 root, score: 79.962	N	N	N	N
vg1127976664	G -> DEL	N	N	silent_mutation	Average:30.267; most accessible tissue: Zhenshan97 root, score: 79.962	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127976664	8.39E-07	1.62E-10	mr1549_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
vg1127976664	NA	2.46E-09	mr1757_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