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Detailed information for vg0812013995:

Variant ID: vg0812013995 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 12013995
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGCATGCTTAAAACTCTGTATAGTTGTCGTTTTTGTGCTTAGAATAGGTTTTAGTGGGCCTAGGAAAAATTTGGTGGCCTGCCGGACCCACCAGGGTTC[A/G]
GCCGAACCAAAACCAGGGCGCGCCCGTTCAGCCCCATTTTTGAACAGTAGTCTCCCCCACTCGTCTTGAGTCTGTTTAGATGCGAGTTCGGAGGTAGATC

Reverse complement sequence

GATCTACCTCCGAACTCGCATCTAAACAGACTCAAGACGAGTGGGGGAGACTACTGTTCAAAAATGGGGCTGAACGGGCGCGCCCTGGTTTTGGTTCGGC[T/C]
GAACCCTGGTGGGTCCGGCAGGCCACCAAATTTTTCCTAGGCCCACTAAAACCTATTCTAAGCACAAAAACGACAACTATACAGAGTTTTAAGCATGCAT

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	56.70%	28.70%	2.48%	12.10%	NA
All Indica	2759	77.20%	12.80%	2.17%	7.83%	NA
All Japonica	1512	15.80%	59.30%	3.64%	21.23%	NA
Aus	269	97.00%	1.10%	0.00%	1.86%	NA
Indica I	595	66.70%	16.50%	2.35%	14.45%	NA
Indica II	465	81.10%	12.00%	1.51%	5.38%	NA
Indica III	913	82.00%	10.60%	2.63%	4.71%	NA
Indica Intermediate	786	77.10%	13.10%	1.91%	7.89%	NA
Temperate Japonica	767	4.30%	68.80%	2.61%	24.25%	NA
Tropical Japonica	504	32.30%	45.40%	4.96%	17.26%	NA
Japonica Intermediate	241	17.80%	58.10%	4.15%	19.92%	NA
VI/Aromatic	96	12.50%	64.60%	0.00%	22.92%	NA
Intermediate	90	43.30%	45.60%	2.22%	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
vg0812013995	A -> G	LOC_Os08g20040.1	downstream_gene_variant ; 3442.0bp to feature; MODIFIER	silent_mutation	Average:50.087; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N
vg0812013995	A -> G	LOC_Os08g20050.1	intron_variant ; MODIFIER	silent_mutation	Average:50.087; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N
vg0812013995	A -> DEL	N	N	silent_mutation	Average:50.087; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0812013995	NA	2.05E-07	mr1238	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
vg0812013995	NA	5.94E-06	mr1309	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
vg0812013995	NA	3.09E-06	mr1422	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
vg0812013995	NA	4.44E-07	mr1583	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
vg0812013995	NA	2.45E-06	mr1735	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
vg0812013995	2.85E-07	2.96E-09	mr1841	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
vg0812013995	NA	9.11E-06	mr1866	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
vg0812013995	NA	2.90E-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
vg0812013995	3.40E-06	3.40E-06	mr1900	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
vg0812013995	7.72E-06	5.96E-28	mr1238_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
vg0812013995	NA	2.06E-10	mr1595_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
vg0812013995	NA	1.92E-08	mr1600_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
vg0812013995	2.22E-06	2.93E-32	mr1841_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
vg0812013995	NA	7.34E-07	mr1841_2	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
vg0812013995	NA	4.84E-20	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