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Detailed information for vg0918621961:

Variant ID: vg0918621961 (JBrowse)	Variation Type: INDEL
Chromosome: chr09	Position: 18621961
Reference Allele: C	Alternative Allele: CT,T
Primary Allele: C	Secondary Allele: CT

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

CTCTCTCCTTGGTTCCTTCAAACCGATTCTCAAATTCGAATTCAACCTCTTAGGTTTTGATTCATCTATCTTTCTCTCTGTATTGGTTCATCAATCTACC[C/CT,T]
TGTTTTCTTTCTCGAACTTCTGACCCAAGTCTGAATATGCAAATCGAGATCACTTCCACCCTTGAACTCTAAATCCCAAGATTCAATCCCCTTCGCCTTG

Reverse complement sequence

CAAGGCGAAGGGGATTGAATCTTGGGATTTAGAGTTCAAGGGTGGAAGTGATCTCGATTTGCATATTCAGACTTGGGTCAGAAGTTCGAGAAAGAAAACA[G/AG,A]
GGTAGATTGATGAACCAATACAGAGAGAAAGATAGATGAATCAAAACCTAAGAGGTTGAATTCGAATTTGAGAATCGGTTTGAAGGAACCAAGGAGAGAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of CT(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	39.60%	22.60%	4.21%	33.20%	T: 0.36%
All Indica	2759	5.10%	37.20%	4.75%	52.37%	T: 0.62%
All Japonica	1512	97.50%	0.10%	0.20%	2.18%	NA
Aus	269	43.90%	13.00%	20.45%	22.68%	NA
Indica I	595	3.40%	29.10%	6.39%	59.83%	T: 1.34%
Indica II	465	4.90%	37.60%	3.44%	53.76%	T: 0.22%
Indica III	913	3.20%	48.10%	2.08%	46.44%	T: 0.22%
Indica Intermediate	786	8.80%	30.30%	7.38%	52.80%	T: 0.76%
Temperate Japonica	767	98.00%	0.30%	0.13%	1.56%	NA
Tropical Japonica	504	96.60%	0.00%	0.20%	3.17%	NA
Japonica Intermediate	241	97.50%	0.00%	0.41%	2.07%	NA
VI/Aromatic	96	78.10%	2.10%	4.17%	15.62%	NA
Intermediate	90	71.10%	5.60%	6.67%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0918621961	C -> CT	LOC_Os09g30494.1	upstream_gene_variant ; 4401.0bp to feature; MODIFIER	silent_mutation	Average:22.013; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N
vg0918621961	C -> CT	LOC_Os09g30490.1	downstream_gene_variant ; 3161.0bp to feature; MODIFIER	silent_mutation	Average:22.013; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N
vg0918621961	C -> CT	LOC_Os09g30490-LOC_Os09g30494	intergenic_region ; MODIFIER	silent_mutation	Average:22.013; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N
vg0918621961	C -> DEL	N	N	silent_mutation	Average:22.013; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N
vg0918621961	C -> T	LOC_Os09g30494.1	upstream_gene_variant ; 4402.0bp to feature; MODIFIER	silent_mutation	Average:22.013; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N
vg0918621961	C -> T	LOC_Os09g30490.1	downstream_gene_variant ; 3160.0bp to feature; MODIFIER	silent_mutation	Average:22.013; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N
vg0918621961	C -> T	LOC_Os09g30490-LOC_Os09g30494	intergenic_region ; MODIFIER	silent_mutation	Average:22.013; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0918621961	4.28E-06	8.65E-07	mr1344	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
vg0918621961	6.28E-06	6.28E-06	mr1356	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
vg0918621961	NA	3.51E-06	mr1511	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
vg0918621961	NA	9.08E-06	mr1642	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
vg0918621961	8.19E-06	3.14E-07	mr1679	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
vg0918621961	8.68E-07	7.09E-08	mr1745	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
vg0918621961	3.11E-06	3.11E-06	mr1783	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
vg0918621961	1.03E-06	6.66E-07	mr1798	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