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Detailed information for vg1109075002:

Variant ID: vg1109075002 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9075002
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.73, A: 0.26, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

TATGTAAATAGGACTTGTATGGGAAAAGCATTGTTTCTAGAGCCTAGACTGCTAAGCTAAAGCTAGTTTATTTATGCTCTGAGCTGAATATAAGCAAACC[C/A]
TTTCTGTTGCTTCTCTGTAGTTAAGTTGTTTACTAAGCCAGATTGAGGACATATGCACCAGGAATCTGTAACCTTCCTCATAAATCAGTAATATCAGCAT

Reverse complement sequence

ATGCTGATATTACTGATTTATGAGGAAGGTTACAGATTCCTGGTGCATATGTCCTCAATCTGGCTTAGTAAACAACTTAACTACAGAGAAGCAACAGAAA[G/T]
GGTTTGCTTATATTCAGCTCAGAGCATAAATAAACTAGCTTTAGCTTAGCAGTCTAGGCTCTAGAAACAATGCTTTTCCCATACAAGTCCTATTTACATA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.10%	28.80%	0.13%	0.00%	NA
All Indica	2759	90.80%	9.20%	0.00%	0.00%	NA
All Japonica	1512	47.70%	52.20%	0.13%	0.00%	NA
Aus	269	18.60%	81.40%	0.00%	0.00%	NA
Indica I	595	93.90%	6.10%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	83.60%	16.40%	0.00%	0.00%	NA
Indica Intermediate	786	91.90%	8.10%	0.00%	0.00%	NA
Temperate Japonica	767	53.60%	46.40%	0.00%	0.00%	NA
Tropical Japonica	504	42.90%	56.70%	0.40%	0.00%	NA
Japonica Intermediate	241	39.00%	61.00%	0.00%	0.00%	NA
VI/Aromatic	96	14.60%	84.40%	1.04%	0.00%	NA
Intermediate	90	75.60%	21.10%	3.33%	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
vg1109075002	C -> A	LOC_Os11g16420.1	downstream_gene_variant ; 4174.0bp to feature; MODIFIER	silent_mutation	Average:52.949; most accessible tissue: Callus, score: 70.791	N	N	N	N
vg1109075002	C -> A	LOC_Os11g16420.2	downstream_gene_variant ; 4174.0bp to feature; MODIFIER	silent_mutation	Average:52.949; most accessible tissue: Callus, score: 70.791	N	N	N	N
vg1109075002	C -> A	LOC_Os11g16410.1	intron_variant ; MODIFIER	silent_mutation	Average:52.949; most accessible tissue: Callus, score: 70.791	N	N	N	N
vg1109075002	C -> A	LOC_Os11g16410.4	intron_variant ; MODIFIER	silent_mutation	Average:52.949; most accessible tissue: Callus, score: 70.791	N	N	N	N
vg1109075002	C -> A	LOC_Os11g16410.3	intron_variant ; MODIFIER	silent_mutation	Average:52.949; most accessible tissue: Callus, score: 70.791	N	N	N	N
vg1109075002	C -> A	LOC_Os11g16410.5	intron_variant ; MODIFIER	silent_mutation	Average:52.949; most accessible tissue: Callus, score: 70.791	N	N	N	N
vg1109075002	C -> A	LOC_Os11g16410.2	intron_variant ; MODIFIER	silent_mutation	Average:52.949; most accessible tissue: Callus, score: 70.791	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109075002	NA	1.71E-07	mr1010_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
vg1109075002	NA	4.24E-06	mr1361_2	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