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Detailed information for vg1126171702:

Variant ID: vg1126171702 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26171702
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, A: 0.13, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

ATGCATGTGCCGGTACATCGGCCGAGATGCCTCCCGTAAATCATGATCTACTCATATGCATGCATATTCATATATTATCATGACCTTACGTATGCATATA[C/A]
TAGGGCAACTTGTGGAGTTGTGGTACAACTACCTCCGGTGACAACGCTCGGATTCAGAGGTATCATCAACTACCTGGTTTTTCTTGGGGTAAAAATGGTT

Reverse complement sequence

AACCATTTTTACCCCAAGAAAAACCAGGTAGTTGATGATACCTCTGAATCCGAGCGTTGTCACCGGAGGTAGTTGTACCACAACTCCACAAGTTGCCCTA[G/T]
TATATGCATACGTAAGGTCATGATAATATATGAATATGCATGCATATGAGTAGATCATGATTTACGGGAGGCATCTCGGCCGATGTACCGGCACATGCAT

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	74.00%	19.60%	1.42%	4.95%	NA
All Indica	2759	82.40%	7.00%	2.36%	8.26%	NA
All Japonica	1512	57.50%	42.30%	0.00%	0.20%	NA
Aus	269	76.60%	23.40%	0.00%	0.00%	NA
Indica I	595	91.90%	7.40%	0.17%	0.50%	NA
Indica II	465	91.20%	4.30%	0.22%	4.30%	NA
Indica III	913	72.00%	6.40%	5.70%	15.99%	NA
Indica Intermediate	786	82.20%	8.90%	1.40%	7.51%	NA
Temperate Japonica	767	46.00%	53.80%	0.00%	0.13%	NA
Tropical Japonica	504	75.60%	24.00%	0.00%	0.40%	NA
Japonica Intermediate	241	56.00%	44.00%	0.00%	0.00%	NA
VI/Aromatic	96	82.30%	15.60%	2.08%	0.00%	NA
Intermediate	90	78.90%	17.80%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1126171702	C -> A	LOC_Os11g43360.1	upstream_gene_variant ; 1442.0bp to feature; MODIFIER	silent_mutation	Average:60.12; most accessible tissue: Callus, score: 94.4	N	N	N	N
vg1126171702	C -> A	LOC_Os11g43350.1	downstream_gene_variant ; 3494.0bp to feature; MODIFIER	silent_mutation	Average:60.12; most accessible tissue: Callus, score: 94.4	N	N	N	N
vg1126171702	C -> A	LOC_Os11g43360-LOC_Os11g43370	intergenic_region ; MODIFIER	silent_mutation	Average:60.12; most accessible tissue: Callus, score: 94.4	N	N	N	N
vg1126171702	C -> DEL	N	N	silent_mutation	Average:60.12; most accessible tissue: Callus, score: 94.4	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126171702	1.97E-07	NA	mr1862	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