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Detailed information for vg1117649044:

Variant ID: vg1117649044 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 17649044
Reference Allele: C	Alternative Allele: T,CCGGAACT
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

AGTCTTAAGGATTATATATTGTATAAAAGATCTAAATAATCTTTACTCACTAAAGTAGTGATCTTTAGTCCCGGTTGGTGGCCCCGTGACAGGCCACTGA[C/T,CCGGAACT]
AGGGGATGAACCGGAACTAAAGATAACACCAATCGGGACTAAAGATCACATAGCTTTTAACAGGCTTTTTTTTCCTGGTTCTTATTAAAACCGGACTATT

Reverse complement sequence

AATAGTCCGGTTTTAATAAGAACCAGGAAAAAAAAGCCTGTTAAAAGCTATGTGATCTTTAGTCCCGATTGGTGTTATCTTTAGTTCCGGTTCATCCCCT[G/A,AGTTCCGG]
TCAGTGGCCTGTCACGGGGCCACCAACCGGGACTAAAGATCACTACTTTAGTGAGTAAAGATTATTTAGATCTTTTATACAATATATAATCCTTAAGACT

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	58.20%	40.90%	0.40%	0.00%	CCGGAACT: 0.44%
All Indica	2759	43.70%	55.00%	0.65%	0.00%	CCGGAACT: 0.62%
All Japonica	1512	90.70%	9.30%	0.07%	0.00%	NA
Aus	269	10.00%	88.80%	0.00%	0.00%	CCGGAACT: 1.12%
Indica I	595	35.00%	64.50%	0.50%	0.00%	NA
Indica II	465	47.10%	52.30%	0.65%	0.00%	NA
Indica III	913	48.70%	49.90%	0.44%	0.00%	CCGGAACT: 0.88%
Indica Intermediate	786	42.50%	55.30%	1.02%	0.00%	CCGGAACT: 1.15%
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	76.40%	23.60%	0.00%	0.00%	NA
Japonica Intermediate	241	93.80%	5.80%	0.41%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	63.30%	35.60%	0.00%	0.00%	CCGGAACT: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1117649044	C -> T	LOC_Os11g30370-LOC_Os11g30390	intergenic_region ; MODIFIER	silent_mutation	Average:63.786; most accessible tissue: Minghui63 root, score: 82.511	N	N	N	N
vg1117649044	C -> CCGGAACT	LOC_Os11g30370-LOC_Os11g30390	intergenic_region ; MODIFIER	silent_mutation	Average:63.786; most accessible tissue: Minghui63 root, score: 82.511	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117649044	NA	4.16E-06	mr1073	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
vg1117649044	NA	1.15E-07	mr1190	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
vg1117649044	NA	4.65E-08	mr1278	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
vg1117649044	NA	2.70E-06	mr1382	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
vg1117649044	NA	3.15E-06	mr1445	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
vg1117649044	NA	3.45E-06	mr1516	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
vg1117649044	NA	2.61E-06	mr1800	Ind_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
vg1117649044	3.99E-06	NA	mr1826	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
vg1117649044	NA	4.94E-08	mr1979	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