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Detailed information for vg1104144721:

Variant ID: vg1104144721 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 4144721
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

CATCGCTTTGCACTTTCCCCTTATGGAGTAAGGCATTCACAATGTCAGGCGAGCCGGCAACCACGGCGATGTGGAGCGGCGTGTTCCCAACCCCGTCCTG[C/T]
GCGTCCAGAAGGCCACCGACCTGCTTGTGTTTCTTGATAGCGAGGGACACGATCGAGGACTGCTTCTCCCTGACCGCGGTGTGCAGGAAGGTCTCTCCAT

Reverse complement sequence

ATGGAGAGACCTTCCTGCACACCGCGGTCAGGGAGAAGCAGTCCTCGATCGTGTCCCTCGCTATCAAGAAACACAAGCAGGTCGGTGGCCTTCTGGACGC[G/A]
CAGGACGGGGTTGGGAACACGCCGCTCCACATCGCCGTGGTTGCCGGCTCGCCTGACATTGTGAATGCCTTACTCCATAAGGGGAAAGTGCAAAGCGATG

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	60.60%	38.40%	0.21%	0.85%	NA
All Indica	2759	87.70%	10.90%	0.29%	1.09%	NA
All Japonica	1512	12.40%	87.10%	0.07%	0.46%	NA
Aus	269	40.90%	58.70%	0.00%	0.37%	NA
Indica I	595	77.60%	19.70%	0.50%	2.18%	NA
Indica II	465	92.90%	5.20%	0.22%	1.72%	NA
Indica III	913	91.20%	8.50%	0.00%	0.22%	NA
Indica Intermediate	786	88.00%	10.60%	0.51%	0.89%	NA
Temperate Japonica	767	1.00%	99.00%	0.00%	0.00%	NA
Tropical Japonica	504	31.00%	67.50%	0.20%	1.39%	NA
Japonica Intermediate	241	9.50%	90.50%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	62.20%	34.40%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1104144721	C -> T	LOC_Os11g07970.1	upstream_gene_variant ; 4242.0bp to feature; MODIFIER	silent_mutation	Average:58.096; most accessible tissue: Callus, score: 81.544	N	N	N	N
vg1104144721	C -> T	LOC_Os11g07970-LOC_Os11g07980	intergenic_region ; MODIFIER	silent_mutation	Average:58.096; most accessible tissue: Callus, score: 81.544	N	N	N	N
vg1104144721	C -> DEL	N	N	silent_mutation	Average:58.096; most accessible tissue: Callus, score: 81.544	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1104144721	NA	4.27E-06	mr1027	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
vg1104144721	NA	5.16E-06	mr1188	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
vg1104144721	3.61E-10	3.70E-12	mr1218	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
vg1104144721	4.85E-06	8.41E-09	mr1422	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
vg1104144721	1.00E-06	1.24E-11	mr1583	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
vg1104144721	NA	7.70E-07	mr1638	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
vg1104144721	NA	4.29E-06	mr1794	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
vg1104144721	1.35E-06	1.35E-06	mr1850	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
vg1104144721	NA	1.49E-07	mr1188_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
vg1104144721	9.19E-09	3.64E-12	mr1218_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
vg1104144721	NA	2.65E-07	mr1583_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
vg1104144721	3.04E-08	1.67E-14	mr1850_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