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Detailed information for vg1120471729:

Variant ID: vg1120471729 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 20471729
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCAAAAAAATTCCGAGCGTACAAGCTCAATCATTACATACAAGTTTACAAACAAAAGTAGCACATAAGCTCGAGCACCTTACATAACACTGAAAGAGTA[G/A]
AAAGACTCCAACACCGTTCAAGGTGAAAAGACTTTCCAAATAAACCAACAACCACATTACTCCATTAACTGCTTTCTCCTGTTCCATCCATCTTTATTAC

Reverse complement sequence

GTAATAAAGATGGATGGAACAGGAGAAAGCAGTTAATGGAGTAATGTGGTTGTTGGTTTATTTGGAAAGTCTTTTCACCTTGAACGGTGTTGGAGTCTTT[C/T]
TACTCTTTCAGTGTTATGTAAGGTGCTCGAGCTTATGTGCTACTTTTGTTTGTAAACTTGTATGTAATGATTGAGCTTGTACGCTCGGAATTTTTTTGGC

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	72.80%	4.30%	0.87%	22.05%	NA
All Indica	2759	69.10%	0.30%	0.80%	29.83%	NA
All Japonica	1512	81.90%	12.50%	0.00%	5.62%	NA
Aus	269	51.30%	0.00%	6.69%	42.01%	NA
Indica I	595	53.40%	0.30%	1.34%	44.87%	NA
Indica II	465	79.40%	0.00%	0.86%	19.78%	NA
Indica III	913	67.30%	0.30%	0.77%	31.65%	NA
Indica Intermediate	786	77.10%	0.30%	0.38%	22.26%	NA
Temperate Japonica	767	73.10%	22.90%	0.00%	3.91%	NA
Tropical Japonica	504	88.90%	1.00%	0.00%	10.12%	NA
Japonica Intermediate	241	95.00%	3.30%	0.00%	1.66%	NA
VI/Aromatic	96	85.40%	0.00%	1.04%	13.54%	NA
Intermediate	90	83.30%	7.80%	0.00%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1120471729	G -> A	LOC_Os11g34930.1	upstream_gene_variant ; 1227.0bp to feature; MODIFIER	silent_mutation	Average:39.881; most accessible tissue: Callus, score: 73.536	N	N	N	N
vg1120471729	G -> A	LOC_Os11g34930-LOC_Os11g34940	intergenic_region ; MODIFIER	silent_mutation	Average:39.881; most accessible tissue: Callus, score: 73.536	N	N	N	N
vg1120471729	G -> DEL	N	N	silent_mutation	Average:39.881; most accessible tissue: Callus, score: 73.536	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120471729	NA	5.71E-08	mr1031_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
vg1120471729	5.50E-06	5.50E-06	mr1193_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
vg1120471729	NA	8.70E-06	mr1321_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
vg1120471729	NA	2.89E-06	mr1354_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
vg1120471729	NA	3.22E-06	mr1428_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
vg1120471729	NA	3.49E-07	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
vg1120471729	NA	5.07E-06	mr1567_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
vg1120471729	1.14E-06	1.19E-07	mr1577_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
vg1120471729	8.06E-06	8.06E-06	mr1587_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
vg1120471729	NA	2.76E-07	mr1723_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
vg1120471729	NA	5.92E-06	mr1740_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
vg1120471729	NA	3.06E-08	mr1768_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
vg1120471729	NA	1.41E-06	mr1792_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
vg1120471729	NA	4.47E-06	mr1829_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
vg1120471729	NA	7.39E-07	mr1902_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