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Detailed information for vg1109530326:

Variant ID: vg1109530326 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9530326
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, T: 0.26, others allele: 0.00, population size: 47. )

Flanking Sequence (100 bp) in Reference Genome:

CCGCAAGAAATATAATCTTCGACCGTAACCATACGGCCTAAGATGGGTTCGGGTTCAATACCTCCTATCTCCCTCTGCATGGTCCCGCGGCCAGGGAGGG[T/C]
GCCGTCGTCCTGCAACTTCTTCAGGGATGCGGTGGTGGAGGTGGACTTGTCGATATCCATCGCCGCCGGAGGATCGCCGGAGAGTAAAGCGAAAGAGGCA

Reverse complement sequence

TGCCTCTTTCGCTTTACTCTCCGGCGATCCTCCGGCGGCGATGGATATCGACAAGTCCACCTCCACCACCGCATCCCTGAAGAAGTTGCAGGACGACGGC[A/G]
CCCTCCCTGGCCGCGGGACCATGCAGAGGGAGATAGGAGGTATTGAACCCGAACCCATCTTAGGCCGTATGGTTACGGTCGAAGATTATATTTCTTGCGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	34.90%	14.80%	4.57%	45.70%	NA
All Indica	2759	5.00%	24.80%	6.85%	63.32%	NA
All Japonica	1512	95.50%	0.30%	0.40%	3.77%	NA
Aus	269	5.20%	1.50%	6.69%	86.62%	NA
Indica I	595	8.70%	15.30%	4.20%	71.76%	NA
Indica II	465	3.70%	19.10%	7.96%	69.25%	NA
Indica III	913	1.80%	38.60%	8.32%	51.37%	NA
Indica Intermediate	786	6.90%	19.30%	6.49%	67.30%	NA
Temperate Japonica	767	96.70%	0.40%	0.26%	2.61%	NA
Tropical Japonica	504	93.80%	0.40%	0.60%	5.16%	NA
Japonica Intermediate	241	95.00%	0.00%	0.41%	4.56%	NA
VI/Aromatic	96	18.80%	0.00%	1.04%	80.21%	NA
Intermediate	90	38.90%	7.80%	2.22%	51.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109530326	T -> DEL	LOC_Os11g17160.1	N	frameshift_variant	Average:18.343; most accessible tissue: Minghui63 root, score: 33.152	N	N	N	N
vg1109530326	T -> C	LOC_Os11g17160.1	missense_variant ; p.Thr21Ala; MODERATE	nonsynonymous_codon ; T21A	Average:18.343; most accessible tissue: Minghui63 root, score: 33.152	benign	-0.383	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109530326	1.95E-06	1.95E-06	mr1025_2	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
vg1109530326	NA	6.83E-07	mr1027_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
vg1109530326	NA	9.25E-06	mr1243_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
vg1109530326	1.56E-06	1.58E-06	mr1306_2	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
vg1109530326	NA	1.74E-07	mr1376_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
vg1109530326	9.55E-06	2.48E-06	mr1409_2	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
vg1109530326	NA	1.02E-07	mr1431_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
vg1109530326	3.60E-06	3.60E-06	mr1463_2	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
vg1109530326	4.25E-06	2.33E-06	mr1505_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
vg1109530326	NA	1.19E-12	mr1521_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
vg1109530326	NA	7.17E-06	mr1554_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
vg1109530326	1.36E-06	NA	mr1558_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
vg1109530326	NA	8.48E-10	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
vg1109530326	NA	6.16E-06	mr1649_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
vg1109530326	6.38E-06	5.45E-06	mr1787_2	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