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Detailed information for vg0711805910:

Variant ID: vg0711805910 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11805910
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGATCGGCTGAGTCTGAGTCGAGCTAAATAAGCCGATATAGCCGATTCCGACAATACGACTTGTACGCGACATCGGGTTCAAGTTGATGTATTTCAAGAT[A/G]
ATTGCCACGCATGGATAGAGTCCTAGGAAGGCAATTGTATCTATTAATTAAGATATTTTATGTAAATCCCTTATAGATAAGTGTGGGCAAAAGTCTGCCG

Reverse complement sequence

CGGCAGACTTTTGCCCACACTTATCTATAAGGGATTTACATAAAATATCTTAATTAATAGATACAATTGCCTTCCTAGGACTCTATCCATGCGTGGCAAT[T/C]
ATCTTGAAATACATCAACTTGAACCCGATGTCGCGTACAAGTCGTATTGTCGGAATCGGCTATATCGGCTTATTTAGCTCGACTCAGACTCAGCCGATCC

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	65.80%	25.40%	0.21%	8.63%	NA
All Indica	2759	97.00%	1.30%	0.00%	1.67%	NA
All Japonica	1512	6.40%	74.90%	0.33%	18.39%	NA
Aus	269	94.80%	0.40%	0.00%	4.83%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	97.00%	3.00%	0.00%	0.00%	NA
Indica III	913	99.60%	0.30%	0.00%	0.11%	NA
Indica Intermediate	786	92.00%	2.30%	0.00%	5.73%	NA
Temperate Japonica	767	2.10%	66.50%	0.52%	30.90%	NA
Tropical Japonica	504	13.70%	85.70%	0.00%	0.60%	NA
Japonica Intermediate	241	5.00%	78.80%	0.41%	15.77%	NA
VI/Aromatic	96	26.00%	0.00%	4.17%	69.79%	NA
Intermediate	90	60.00%	34.40%	1.11%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0711805910	A -> DEL	N	N	silent_mutation	Average:45.991; most accessible tissue: Zhenshan97 flag leaf, score: 63.67	N	N	N	N
vg0711805910	A -> G	LOC_Os07g20430.1	upstream_gene_variant ; 2279.0bp to feature; MODIFIER	silent_mutation	Average:45.991; most accessible tissue: Zhenshan97 flag leaf, score: 63.67	N	N	N	N
vg0711805910	A -> G	LOC_Os07g20450.1	downstream_gene_variant ; 4148.0bp to feature; MODIFIER	silent_mutation	Average:45.991; most accessible tissue: Zhenshan97 flag leaf, score: 63.67	N	N	N	N
vg0711805910	A -> G	LOC_Os07g20440.1	intron_variant ; MODIFIER	silent_mutation	Average:45.991; most accessible tissue: Zhenshan97 flag leaf, score: 63.67	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711805910	NA	1.72E-07	mr1004_2	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
vg0711805910	1.47E-06	1.27E-27	mr1024_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
vg0711805910	NA	3.63E-08	mr1084_2	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
vg0711805910	NA	1.04E-15	mr1118_2	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
vg0711805910	NA	1.10E-16	mr1146_2	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
vg0711805910	NA	8.34E-15	mr1148_2	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
vg0711805910	NA	1.05E-07	mr1205_2	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
vg0711805910	NA	2.70E-13	mr1217_2	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
vg0711805910	NA	3.05E-19	mr1239_2	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
vg0711805910	NA	7.97E-25	mr1242_2	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
vg0711805910	NA	7.56E-07	mr1275_2	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
vg0711805910	NA	2.43E-13	mr1496_2	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
vg0711805910	NA	4.41E-14	mr1575_2	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
vg0711805910	NA	7.30E-10	mr1646_2	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
vg0711805910	NA	9.15E-33	mr1723_2	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
vg0711805910	NA	1.04E-32	mr1873_2	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
vg0711805910	NA	5.41E-21	mr1922_2	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
vg0711805910	NA	9.13E-15	mr1936_2	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
vg0711805910	NA	1.37E-08	mr1940_2	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