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Detailed information for vg1127876436:

Variant ID: vg1127876436 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27876436
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCCGATAGCGTATCATTGGTGGTCTCAGCCGATGGGGTTAGACCAAATCGGCTATGGATTGGATATATCAAAGAATAATAAACCCTAAATATGTCTCAT[C/T]
GGCTGTAACACTGTCTATCAAGATTGATAAAGAAGCTTAAGAAAATATTATTAAAATAGCCGATGTAACAGTATTTAGAGCAATAACGATAATGTACTAG

Reverse complement sequence

CTAGTACATTATCGTTATTGCTCTAAATACTGTTACATCGGCTATTTTAATAATATTTTCTTAAGCTTCTTTATCAATCTTGATAGACAGTGTTACAGCC[G/A]
ATGAGACATATTTAGGGTTTATTATTCTTTGATATATCCAATCCATAGCCGATTTGGTCTAACCCCATCGGCTGAGACCACCAATGATACGCTATCGGCC

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	66.40%	3.30%	19.28%	11.05%	NA
All Indica	2759	65.30%	2.80%	25.88%	5.94%	NA
All Japonica	1512	68.50%	3.90%	5.22%	22.35%	NA
Aus	269	69.10%	0.70%	26.77%	3.35%	NA
Indica I	595	54.30%	4.00%	26.39%	15.29%	NA
Indica II	465	71.20%	1.70%	23.01%	4.09%	NA
Indica III	913	70.80%	2.70%	25.41%	1.10%	NA
Indica Intermediate	786	64.00%	2.70%	27.74%	5.60%	NA
Temperate Japonica	767	57.60%	1.00%	4.82%	36.51%	NA
Tropical Japonica	504	85.90%	4.60%	4.56%	4.96%	NA
Japonica Intermediate	241	66.80%	11.60%	7.88%	13.69%	NA
VI/Aromatic	96	43.80%	15.60%	34.38%	6.25%	NA
Intermediate	90	76.70%	3.30%	14.44%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127876436	C -> T	LOC_Os11g46050.1	downstream_gene_variant ; 4800.0bp to feature; MODIFIER	silent_mutation	Average:39.703; most accessible tissue: Minghui63 young leaf, score: 72.959	N	N	N	N
vg1127876436	C -> T	LOC_Os11g46050-LOC_Os11g46060	intergenic_region ; MODIFIER	silent_mutation	Average:39.703; most accessible tissue: Minghui63 young leaf, score: 72.959	N	N	N	N
vg1127876436	C -> DEL	N	N	silent_mutation	Average:39.703; most accessible tissue: Minghui63 young leaf, score: 72.959	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127876436	1.55E-06	1.55E-06	mr1234	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
vg1127876436	NA	5.67E-06	mr1519	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