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Detailed information for vg1119557203:

Variant ID: vg1119557203 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19557203
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATGCTTTCTATATATAAATGTATTGCAAAACTGTTTTAAAGTCCAATTTTCAACATAATTCATACACTGATAGAGAAACCATCTTTGGTCGGTCGACCC[C/A]
AATCCACAATAGTCCCGGTTCCATTAAAAACCGGGACAAAATGATTTTTAGTCCCGGTTAATAAGAGGAAGATCTTTAGTCCCGGTTGTTGTTACCAACC

Reverse complement sequence

GGTTGGTAACAACAACCGGGACTAAAGATCTTCCTCTTATTAACCGGGACTAAAAATCATTTTGTCCCGGTTTTTAATGGAACCGGGACTATTGTGGATT[G/T]
GGGTCGACCGACCAAAGATGGTTTCTCTATCAGTGTATGAATTATGTTGAAAATTGGACTTTAAAACAGTTTTGCAATACATTTATATATAGAAAGCATT

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	67.10%	32.50%	0.49%	0.00%	NA
All Indica	2759	96.80%	2.80%	0.47%	0.00%	NA
All Japonica	1512	11.40%	88.20%	0.46%	0.00%	NA
Aus	269	94.40%	5.60%	0.00%	0.00%	NA
Indica I	595	96.80%	2.20%	1.01%	0.00%	NA
Indica II	465	98.30%	1.50%	0.22%	0.00%	NA
Indica III	913	98.60%	1.30%	0.11%	0.00%	NA
Indica Intermediate	786	93.80%	5.60%	0.64%	0.00%	NA
Temperate Japonica	767	7.60%	91.90%	0.52%	0.00%	NA
Tropical Japonica	504	12.30%	87.30%	0.40%	0.00%	NA
Japonica Intermediate	241	21.60%	78.00%	0.41%	0.00%	NA
VI/Aromatic	96	24.00%	76.00%	0.00%	0.00%	NA
Intermediate	90	55.60%	41.10%	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
vg1119557203	C -> A	LOC_Os11g33070.1	upstream_gene_variant ; 2347.0bp to feature; MODIFIER	silent_mutation	Average:30.669; most accessible tissue: Callus, score: 59.439	N	N	N	N
vg1119557203	C -> A	LOC_Os11g33070-LOC_Os11g33080	intergenic_region ; MODIFIER	silent_mutation	Average:30.669; most accessible tissue: Callus, score: 59.439	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119557203	NA	2.80E-12	mr1205	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
vg1119557203	NA	4.41E-08	mr1514	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
vg1119557203	NA	1.38E-10	mr1775	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
vg1119557203	1.48E-06	NA	mr1334_2	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