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Detailed information for vg0406853125:

Variant ID: vg0406853125 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6853125
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

TCGAAAAAGGCTATGTTTTGCAGAATCCCGAAGATCCCACCAAGGAGGACGACGAGAACGAGCACAAGAACGCTCAAGCCGCTAATGCAATACTTAGCGC[C/G]
TTGAGTGAAAGTGAGTTCAACTGTGTGGATGGCATTGAGAGTGCCAAAGTGATTTGGGACACGCTTCAGAACTTGCATGAAGGCACGAATAGTGTTCGTG

Reverse complement sequence

CACGAACACTATTCGTGCCTTCATGCAAGTTCTGAAGCGTGTCCCAAATCACTTTGGCACTCTCAATGCCATCCACACAGTTGAACTCACTTTCACTCAA[G/C]
GCGCTAAGTATTGCATTAGCGGCTTGAGCGTTCTTGTGCTCGTTCTCGTCGTCCTCCTTGGTGGGATCTTCGGGATTCTGCAAAACATAGCCTTTTTCGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.20%	10.90%	3.51%	11.45%	NA
All Indica	2759	62.50%	18.10%	5.69%	13.77%	NA
All Japonica	1512	95.60%	0.30%	0.07%	3.97%	NA
Aus	269	71.70%	0.00%	0.74%	27.51%	NA
Indica I	595	77.00%	6.10%	2.52%	14.45%	NA
Indica II	465	70.50%	15.30%	1.51%	12.69%	NA
Indica III	913	49.70%	23.70%	11.50%	15.12%	NA
Indica Intermediate	786	61.50%	22.40%	3.82%	12.34%	NA
Temperate Japonica	767	97.00%	0.10%	0.00%	2.87%	NA
Tropical Japonica	504	95.20%	0.80%	0.00%	3.97%	NA
Japonica Intermediate	241	92.10%	0.00%	0.41%	7.47%	NA
VI/Aromatic	96	74.00%	0.00%	5.21%	20.83%	NA
Intermediate	90	81.10%	10.00%	1.11%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0406853125	C -> DEL	LOC_Os04g12410.1	N	frameshift_variant	Average:30.113; most accessible tissue: Minghui63 flag leaf, score: 57.188	N	N	N	N
vg0406853125	C -> G	LOC_Os04g12410.1	synonymous_variant ; p.Ala99Ala; LOW	synonymous_codon	Average:30.113; most accessible tissue: Minghui63 flag leaf, score: 57.188	N	N	N	N
vg0406853125	C -> G	LOC_Os04g12410.1	synonymous_variant ; p.Ala99Ala; LOW	nonsynonymous_codon ; A99T	Average:30.113; most accessible tissue: Minghui63 flag leaf, score: 57.188	possibly damaging	1.571	DELETERIOUS	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406853125	NA	5.87E-06	mr1015	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
vg0406853125	7.55E-06	7.55E-06	mr1054	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
vg0406853125	NA	1.08E-06	mr1166	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
vg0406853125	NA	4.02E-09	mr1305	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
vg0406853125	7.94E-06	3.90E-06	mr1320	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
vg0406853125	7.90E-06	7.90E-06	mr1379	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
vg0406853125	NA	4.68E-08	mr1515	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
vg0406853125	NA	7.17E-06	mr1516	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
vg0406853125	NA	6.13E-07	mr1586	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
vg0406853125	NA	2.84E-06	mr1660	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
vg0406853125	4.62E-08	4.43E-08	mr1687	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
vg0406853125	2.83E-08	2.83E-08	mr1687	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
vg0406853125	NA	1.01E-06	mr1765	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
vg0406853125	4.92E-06	4.92E-06	mr1866	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