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Detailed information for vg0706565900:

Variant ID: vg0706565900 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 6565900
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGCGAACGTGGGTGGCTTGGTCCTCATAAACTCTCCAAAGCTCGATCCTCCGCGGTTGCTTTGGTTGTTTGCAATGGCTTGCAGAAGTTGGGTTTGAGT[A/G]
GCCATAACTCCGGCCAGGGTGGTTAGGTCAGGTGTCTGAGTTTCTTCATTGATGGTTGACGCCCGACGTCGGCTGGCCATCTGTGTAGGCCGATAAAGTA

Reverse complement sequence

TACTTTATCGGCCTACACAGATGGCCAGCCGACGTCGGGCGTCAACCATCAATGAAGAAACTCAGACACCTGACCTAACCACCCTGGCCGGAGTTATGGC[T/C]
ACTCAAACCCAACTTCTGCAAGCCATTGCAAACAACCAAAGCAACCGCGGAGGATCGAGCTTTGGAGAGTTTATGAGGACCAAGCCACCCACGTTCGCTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.70%	2.50%	22.43%	0.36%	NA
All Indica	2759	63.20%	3.30%	32.91%	0.58%	NA
All Japonica	1512	99.10%	0.10%	0.79%	0.00%	NA
Aus	269	42.80%	8.20%	48.70%	0.37%	NA
Indica I	595	92.10%	2.70%	5.21%	0.00%	NA
Indica II	465	81.30%	2.20%	16.56%	0.00%	NA
Indica III	913	28.90%	4.40%	65.17%	1.53%	NA
Indica Intermediate	786	70.40%	3.30%	26.08%	0.25%	NA
Temperate Japonica	767	98.60%	0.30%	1.17%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	97.90%	1.00%	1.04%	0.00%	NA
Intermediate	90	90.00%	1.10%	8.89%	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
vg0706565900	A -> DEL	LOC_Os07g11860.1	N	frameshift_variant	Average:13.159; most accessible tissue: Zhenshan97 young leaf, score: 24.604	N	N	N	N
vg0706565900	A -> G	LOC_Os07g11860.1	synonymous_variant ; p.Ala211Ala; LOW	synonymous_codon	Average:13.159; most accessible tissue: Zhenshan97 young leaf, score: 24.604	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0706565900	NA	8.91E-29	mr1075	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
vg0706565900	NA	2.05E-06	mr1085	Ind_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
vg0706565900	NA	1.53E-08	mr1103	Ind_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
vg0706565900	1.63E-06	8.02E-09	mr1104	Ind_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
vg0706565900	NA	3.69E-08	mr1107	Ind_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
vg0706565900	NA	1.59E-09	mr1226	Ind_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
vg0706565900	NA	1.24E-06	mr1437	Ind_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
vg0706565900	NA	3.97E-28	mr1546	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
vg0706565900	NA	1.34E-07	mr1560	Ind_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
vg0706565900	NA	9.33E-19	mr1566	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
vg0706565900	NA	1.71E-31	mr1085_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
vg0706565900	NA	4.04E-36	mr1107_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
vg0706565900	NA	1.62E-24	mr1233_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
vg0706565900	NA	9.76E-17	mr1342_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
vg0706565900	NA	2.95E-17	mr1592_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
vg0706565900	NA	3.23E-22	mr1609_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
vg0706565900	NA	3.32E-19	mr1637_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
vg0706565900	NA	3.90E-07	mr1749_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
vg0706565900	NA	2.21E-19	mr1900_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
vg0706565900	NA	1.80E-18	mr1945_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
vg0706565900	NA	7.61E-09	mr1947_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