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Detailed information for vg1121842515:

Variant ID: vg1121842515 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21842515
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, C: 0.02, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

ACTAGACACTGCAGCTCTTCCAAGTGACTTGGATTCGGCATTTACTTCCATTACTCTTGAATCCTACATGGCTCTTGACAACAAAACAAATATCGAATTA[A/C]
TCAGTTATGTATGCCCTGATTCAGAATTCTACAACTTCGAACAAGACCGCTCGCATGATAAGTTTGAAGCTGGCCAGATTTGGGCTCTTTACAGTGATAC

Reverse complement sequence

GTATCACTGTAAAGAGCCCAAATCTGGCCAGCTTCAAACTTATCATGCGAGCGGTCTTGTTCGAAGTTGTAGAATTCTGAATCAGGGCATACATAACTGA[T/G]
TAATTCGATATTTGTTTTGTTGTCAAGAGCCATGTAGGATTCAAGAGTAATGGAAGTAAATGCCGAATCCAAGTCACTTGGAAGAGCTGCAGTGTCTAGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.90%	39.50%	0.51%	1.04%	NA
All Indica	2759	39.10%	60.00%	0.62%	0.29%	NA
All Japonica	1512	91.10%	6.00%	0.40%	2.51%	NA
Aus	269	68.00%	30.90%	0.37%	0.74%	NA
Indica I	595	59.50%	40.20%	0.34%	0.00%	NA
Indica II	465	31.80%	66.50%	1.51%	0.22%	NA
Indica III	913	32.30%	67.00%	0.44%	0.22%	NA
Indica Intermediate	786	35.90%	63.00%	0.51%	0.64%	NA
Temperate Japonica	767	94.00%	4.70%	0.39%	0.91%	NA
Tropical Japonica	504	85.50%	10.10%	0.40%	3.97%	NA
Japonica Intermediate	241	93.80%	1.20%	0.41%	4.56%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	61.10%	37.80%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121842515	A -> DEL	N	N	silent_mutation	Average:53.198; most accessible tissue: Zhenshan97 flower, score: 85.399	N	N	N	N
vg1121842515	A -> C	LOC_Os11g37000.1	3_prime_UTR_variant ; 652.0bp to feature; MODIFIER	silent_mutation	Average:53.198; most accessible tissue: Zhenshan97 flower, score: 85.399	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121842515	7.68E-07	3.38E-09	mr1698	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
vg1121842515	NA	4.47E-06	mr1517_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
vg1121842515	NA	3.47E-06	mr1698_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