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Detailed information for vg1107619564:

Variant ID: vg1107619564 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 7619564
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTCCCTCTATTTGTCGCCCAGTCCGATTTCCGTGCCTTGACCGCAAAAAGGATACGACTCATCCCCCAACTTCCGAAAACCGGGCAAACGAGGTCCCTC[G/A]
GCGGTTTTGGCTGACGTGGTACCTACATGGCTTGTTTGATTAGTTTTCCATCCCACGTAGCATTGATGTGGTGCTAACGTGACAATTATATCTCAGAAAA

Reverse complement sequence

TTTTCTGAGATATAATTGTCACGTTAGCACCACATCAATGCTACGTGGGATGGAAAACTAATCAAACAAGCCATGTAGGTACCACGTCAGCCAAAACCGC[C/T]
GAGGGACCTCGTTTGCCCGGTTTTCGGAAGTTGGGGGATGAGTCGTATCCTTTTTGCGGTCAAGGCACGGAAATCGGACTGGGCGACAAATAGAGGGACA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.70%	0.40%	1.95%	19.93%	NA
All Indica	2759	97.80%	0.10%	0.94%	1.12%	NA
All Japonica	1512	36.70%	1.00%	3.17%	59.13%	NA
Aus	269	96.30%	0.00%	3.35%	0.37%	NA
Indica I	595	96.80%	0.00%	3.03%	0.17%	NA
Indica II	465	99.60%	0.00%	0.00%	0.43%	NA
Indica III	913	98.90%	0.20%	0.55%	0.33%	NA
Indica Intermediate	786	96.30%	0.10%	0.38%	3.18%	NA
Temperate Japonica	767	43.30%	1.00%	4.04%	51.63%	NA
Tropical Japonica	504	25.80%	1.20%	2.38%	70.63%	NA
Japonica Intermediate	241	38.60%	0.40%	2.07%	58.92%	NA
VI/Aromatic	96	91.70%	0.00%	6.25%	2.08%	NA
Intermediate	90	81.10%	0.00%	3.33%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1107619564	G -> A	LOC_Os11g13830.1	upstream_gene_variant ; 435.0bp to feature; MODIFIER	silent_mutation	Average:77.285; most accessible tissue: Callus, score: 95.947	N	N	N	N
vg1107619564	G -> A	LOC_Os11g13820.1	downstream_gene_variant ; 829.0bp to feature; MODIFIER	silent_mutation	Average:77.285; most accessible tissue: Callus, score: 95.947	N	N	N	N
vg1107619564	G -> A	LOC_Os11g13820-LOC_Os11g13830	intergenic_region ; MODIFIER	silent_mutation	Average:77.285; most accessible tissue: Callus, score: 95.947	N	N	N	N
vg1107619564	G -> DEL	N	N	silent_mutation	Average:77.285; most accessible tissue: Callus, score: 95.947	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1107619564	NA	2.65E-06	mr1622	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
vg1107619564	NA	6.83E-06	mr1807	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
vg1107619564	9.76E-07	NA	mr1672_2	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