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Detailed information for vg0712408577:

Variant ID: vg0712408577 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 12408577
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTGAACAACCTTGCAAGAACTGACCTTGTAAACCATAACCACTATAGGTAGCACTTGTTGCCTCTGGGATTGGGGGTGACTTAGCTGTGCTGGTCTGCT[A/G]
AAGACTTGGTGGCGTACTGTCTGAGGTTGCAGGTGCTTGCTCTTGGAAAACAAACTGACTTTCGCTCTGATCCTGATTCCGGCTTGCATCTGAGCTTGTA

Reverse complement sequence

TACAAGCTCAGATGCAAGCCGGAATCAGGATCAGAGCGAAAGTCAGTTTGTTTTCCAAGAGCAAGCACCTGCAACCTCAGACAGTACGCCACCAAGTCTT[T/C]
AGCAGACCAGCACAGCTAAGTCACCCCCAATCCCAGAGGCAACAAGTGCTACCTATAGTGGTTATGGTTTACAAGGTCAGTTCTTGCAAGGTTGTTCAAC

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	26.40%	8.70%	19.32%	45.58%	NA
All Indica	2759	2.30%	9.60%	18.88%	69.19%	NA
All Japonica	1512	75.50%	7.50%	7.14%	9.85%	NA
Aus	269	1.90%	9.70%	61.71%	26.77%	NA
Indica I	595	2.00%	6.20%	17.14%	74.62%	NA
Indica II	465	3.90%	7.30%	16.34%	72.47%	NA
Indica III	913	1.80%	12.70%	14.13%	71.41%	NA
Indica Intermediate	786	2.30%	9.90%	27.23%	60.56%	NA
Temperate Japonica	767	67.50%	10.30%	5.74%	16.43%	NA
Tropical Japonica	504	86.10%	3.40%	9.92%	0.60%	NA
Japonica Intermediate	241	78.80%	7.10%	5.81%	8.30%	NA
VI/Aromatic	96	0.00%	4.20%	95.83%	0.00%	NA
Intermediate	90	38.90%	5.60%	28.89%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0712408577	A -> DEL	N	N	silent_mutation	Average:39.551; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N
vg0712408577	A -> G	LOC_Os07g22210-LOC_Os07g22220	intergenic_region ; MODIFIER	silent_mutation	Average:39.551; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0712408577	NA	3.72E-20	mr1676	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
vg0712408577	NA	1.30E-13	mr1900	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
vg0712408577	NA	9.82E-10	mr1905	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
vg0712408577	2.02E-06	1.46E-25	mr1042_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
vg0712408577	NA	1.71E-20	mr1167_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
vg0712408577	NA	7.84E-07	mr1369_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
vg0712408577	NA	1.17E-06	mr1418_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
vg0712408577	NA	1.98E-07	mr1453_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
vg0712408577	NA	4.63E-07	mr1479_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
vg0712408577	NA	5.14E-06	mr1574_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
vg0712408577	NA	6.85E-13	mr1636_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
vg0712408577	NA	1.22E-12	mr1641_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
vg0712408577	NA	2.55E-11	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
vg0712408577	NA	9.39E-11	mr1667_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
vg0712408577	NA	1.80E-09	mr1681_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
vg0712408577	NA	9.88E-08	mr1683_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
vg0712408577	NA	2.91E-17	mr1726_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
vg0712408577	NA	2.89E-13	mr1838_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
vg0712408577	NA	4.84E-14	mr1950_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
vg0712408577	NA	8.61E-11	mr1986_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