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Detailed information for vg0719897669:

Variant ID: vg0719897669 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 19897669
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCAGGCTTTTTTTTTGTCTTCTGTATAAGGTTTTCGCCGGTTTTACTTTAGCAAACCGTGCTATTGTATGGTTTTTGGGTCCGGTTTTCCTTATAAATAG[A/G]
TTCAACTCTATCTTTCTAATATATTCGGCAATACTCTTGCCACTTCCACATAAAAAAATGCAGGTCAGAACAGAGGGTAACAATCAAGACACACAGACCA

Reverse complement sequence

TGGTCTGTGTGTCTTGATTGTTACCCTCTGTTCTGACCTGCATTTTTTTATGTGGAAGTGGCAAGAGTATTGCCGAATATATTAGAAAGATAGAGTTGAA[T/C]
CTATTTATAAGGAAAACCGGACCCAAAAACCATACAATAGCACGGTTTGCTAAAGTAAAACCGGCGAAAACCTTATACAGAAGACAAAAAAAAAGCCTGA

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	80.90%	16.90%	0.11%	2.05%	NA
All Indica	2759	99.30%	0.70%	0.00%	0.07%	NA
All Japonica	1512	49.00%	50.50%	0.07%	0.40%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	98.90%	0.90%	0.00%	0.25%	NA
Temperate Japonica	767	47.70%	52.20%	0.00%	0.13%	NA
Tropical Japonica	504	58.30%	41.70%	0.00%	0.00%	NA
Japonica Intermediate	241	33.60%	63.90%	0.41%	2.07%	NA
VI/Aromatic	96	11.50%	2.10%	4.17%	82.29%	NA
Intermediate	90	71.10%	17.80%	0.00%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0719897669	A -> DEL	N	N	silent_mutation	Average:50.261; most accessible tissue: Zhenshan97 root, score: 64.045	N	N	N	N
vg0719897669	A -> G	LOC_Os07g33280.1	upstream_gene_variant ; 1541.0bp to feature; MODIFIER	silent_mutation	Average:50.261; most accessible tissue: Zhenshan97 root, score: 64.045	N	N	N	N
vg0719897669	A -> G	LOC_Os07g33270-LOC_Os07g33280	intergenic_region ; MODIFIER	silent_mutation	Average:50.261; most accessible tissue: Zhenshan97 root, score: 64.045	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0719897669	NA	5.41E-06	mr1020_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
vg0719897669	NA	2.70E-08	mr1030_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
vg0719897669	NA	5.46E-07	mr1173_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
vg0719897669	NA	2.38E-06	mr1187_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
vg0719897669	NA	3.65E-07	mr1452_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
vg0719897669	NA	6.03E-12	mr1666_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
vg0719897669	NA	6.54E-10	mr1709_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
vg0719897669	7.14E-07	1.41E-12	mr1749_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
vg0719897669	1.13E-06	1.20E-13	mr1761_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
vg0719897669	NA	7.48E-06	mr1761_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
vg0719897669	5.04E-08	5.90E-14	mr1821_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
vg0719897669	NA	4.27E-06	mr1821_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
vg0719897669	NA	1.74E-06	mr1875_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