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Detailed information for vg1102879043:

Variant ID: vg1102879043 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 2879043
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.65, T: 0.37, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTTCTTTTATCTATATTTAATGTGCCATGCATGTGTGTCCTAAGATTTGATGTGATGTTTTTGAGTAAATTTTTTTTAACTAAGGCTGTATTTAGATC[T/C]
AAACTTCAGTCATTTTCCATCACATCAACCTGTGATACACACAACTTTTTCAGTCACATCATCTCCAATTTCAACCAAAATCCAAACTTTACGCTGAACT

Reverse complement sequence

AGTTCAGCGTAAAGTTTGGATTTTGGTTGAAATTGGAGATGATGTGACTGAAAAAGTTGTGTGTATCACAGGTTGATGTGATGGAAAATGACTGAAGTTT[A/G]
GATCTAAATACAGCCTTAGTTAAAAAAAATTTACTCAAAAACATCACATCAAATCTTAGGACACACATGCATGGCACATTAAATATAGATAAAAGAAAAA

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	71.70%	28.20%	0.08%	0.00%	NA
All Indica	2759	60.10%	39.70%	0.14%	0.00%	NA
All Japonica	1512	97.00%	3.00%	0.00%	0.00%	NA
Aus	269	37.50%	62.50%	0.00%	0.00%	NA
Indica I	595	36.60%	63.20%	0.17%	0.00%	NA
Indica II	465	75.10%	24.90%	0.00%	0.00%	NA
Indica III	913	68.50%	31.50%	0.00%	0.00%	NA
Indica Intermediate	786	59.40%	40.20%	0.38%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	91.50%	8.50%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	78.90%	21.10%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1102879043	T -> C	LOC_Os11g06050.1	upstream_gene_variant ; 3263.0bp to feature; MODIFIER	silent_mutation	Average:42.152; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg1102879043	T -> C	LOC_Os11g06050-LOC_Os11g06070	intergenic_region ; MODIFIER	silent_mutation	Average:42.152; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1102879043	NA	2.59E-07	mr1598	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
vg1102879043	NA	6.54E-07	mr1835	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
vg1102879043	NA	5.85E-12	mr1904	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
vg1102879043	NA	4.05E-10	mr1835_2	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
vg1102879043	NA	5.30E-14	mr1904_2	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