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Detailed information for vg0810425666:

Variant ID: vg0810425666 (JBrowse)	Variation Type: INDEL
Chromosome: chr08	Position: 10425666
Reference Allele: C	Alternative Allele: A,CA
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

AATTGCTTATGTAGATCAGCTATCTGCAATTGCATTCTGGCTGATCCCATCTTCTCAGCATGCAATTCACTCTCTAGCTCACGTACATGATCATTCATTG[C/A,CA]
AGCAGCTTTGGCATTTTTCTTCATCTCTGTGGACTGCATGCCAACATTGCGAAGAAAAGTTGATTTTGGCAGAACATGAGCTACAGCTTCAACAGGAGTC

Reverse complement sequence

GACTCCTGTTGAAGCTGTAGCTCATGTTCTGCCAAAATCAACTTTTCTTCGCAATGTTGGCATGCAGTCCACAGAGATGAAGAAAAATGCCAAAGCTGCT[G/T,TG]
CAATGAATGATCATGTACGTGAGCTAGAGAGTGAATTGCATGCTGAGAAGATGGGATCAGCCAGAATGCAATTGCAGATAGCTGATCTACATAAGCAATT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.70%	17.60%	4.66%	0.00%	CA: 0.04%
All Indica	2759	71.10%	23.10%	5.80%	0.00%	NA
All Japonica	1512	94.60%	3.00%	2.45%	0.00%	NA
Aus	269	46.80%	47.60%	5.20%	0.00%	CA: 0.37%
Indica I	595	82.50%	13.90%	3.53%	0.00%	NA
Indica II	465	89.70%	6.20%	4.09%	0.00%	NA
Indica III	913	50.80%	41.50%	7.67%	0.00%	NA
Indica Intermediate	786	75.10%	18.60%	6.36%	0.00%	NA
Temperate Japonica	767	98.40%	0.30%	1.30%	0.00%	NA
Tropical Japonica	504	89.10%	6.70%	4.17%	0.00%	NA
Japonica Intermediate	241	93.80%	3.70%	2.49%	0.00%	NA
VI/Aromatic	96	81.20%	13.50%	5.21%	0.00%	NA
Intermediate	90	85.60%	8.90%	4.44%	0.00%	CA: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0810425666	C -> A	LOC_Os08g17020.1	missense_variant ; p.Ala198Ser; MODERATE	nonsynonymous_codon ; A198S	Average:12.249; most accessible tissue: Callus, score: 25.508	unknown	unknown	TOLERATED	0.37
vg0810425666	C -> CA	LOC_Os08g17020.1	frameshift_variant ; p.Ala198fs; HIGH	frameshift_variant	Average:12.249; most accessible tissue: Callus, score: 25.508	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0810425666	NA	1.21E-10	mr1016	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
vg0810425666	NA	3.79E-11	mr1017	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
vg0810425666	NA	3.50E-10	mr1018	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
vg0810425666	NA	2.11E-09	mr1019	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
vg0810425666	NA	3.83E-12	mr1055	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
vg0810425666	NA	1.84E-10	mr1132	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
vg0810425666	NA	5.66E-12	mr1390	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
vg0810425666	NA	1.68E-12	mr1490	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
vg0810425666	2.70E-06	2.28E-11	mr1055_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
vg0810425666	3.30E-06	NA	mr1132_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
vg0810425666	NA	3.04E-14	mr1132_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
vg0810425666	NA	6.06E-13	mr1178_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
vg0810425666	3.08E-07	4.21E-15	mr1390_2	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
vg0810425666	1.38E-07	1.34E-15	mr1490_2	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