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Detailed information for vg1214046223:

Variant ID: vg1214046223 (JBrowse)	Variation Type: INDEL
Chromosome: chr12	Position: 14046223
Reference Allele: C	Alternative Allele: CGGTCATCTTGTTA,T
Primary Allele: C	Secondary Allele: CGGTCATCTTGTTA

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

CTATCAGAGAATAACAGCGGGAGACAAAATAATATAAGGGCCCGGTTGACATGCCACGAGCAGTCGACTAGGGAACGAGACCTAGAACGAAACCACACTC[C/CGGTCATCTTGTTA,T]
GGTCATCTTGTTAGGTATGCAAGCATACTAACAAGGGCTTCTCTTCAACACTCTGCTAAAAGATATATATATAGAGCAACAATGAGTACAAAAGTACTTA

Reverse complement sequence

TAAGTACTTTTGTACTCATTGTTGCTCTATATATATATCTTTTAGCAGAGTGTTGAAGAGAAGCCCTTGTTAGTATGCTTGCATACCTAACAAGATGACC[G/TAACAAGATGACCG,A]
GAGTGTGGTTTCGTTCTAGGTCTCGTTCCCTAGTCGACTGCTCGTGGCATGTCAACCGGGCCCTTATATTATTTTGTCTCCCGCTGTTATTCTCTGATAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of CGGTCATCTTGTTA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.40%	13.60%	0.76%	0.00%	T: 1.25%
All Indica	2759	96.80%	3.10%	0.11%	0.00%	T: 0.04%
All Japonica	1512	62.80%	31.50%	1.92%	0.00%	T: 3.77%
Aus	269	82.20%	17.10%	0.74%	0.00%	NA
Indica I	595	99.50%	0.30%	0.17%	0.00%	NA
Indica II	465	89.50%	10.50%	0.00%	0.00%	NA
Indica III	913	98.40%	1.50%	0.00%	0.00%	T: 0.11%
Indica Intermediate	786	97.20%	2.50%	0.25%	0.00%	NA
Temperate Japonica	767	87.40%	9.40%	1.30%	0.00%	T: 1.96%
Tropical Japonica	504	26.00%	65.70%	2.38%	0.00%	T: 5.95%
Japonica Intermediate	241	61.40%	30.70%	2.90%	0.00%	T: 4.98%
VI/Aromatic	96	80.20%	19.80%	0.00%	0.00%	NA
Intermediate	90	77.80%	18.90%	2.22%	0.00%	T: 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
vg1214046223	C -> CGGTCATCTTGTTA	LOC_Os12g24555.1	upstream_gene_variant ; 1620.0bp to feature; MODIFIER	silent_mutation	Average:42.411; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg1214046223	C -> CGGTCATCTTGTTA	LOC_Os12g24555-LOC_Os12g24580	intergenic_region ; MODIFIER	silent_mutation	Average:42.411; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg1214046223	C -> T	LOC_Os12g24555.1	upstream_gene_variant ; 1619.0bp to feature; MODIFIER	silent_mutation	Average:42.411; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg1214046223	C -> T	LOC_Os12g24555-LOC_Os12g24580	intergenic_region ; MODIFIER	silent_mutation	Average:42.411; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214046223	NA	3.38E-07	mr1156	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
vg1214046223	NA	8.89E-06	mr1164	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
vg1214046223	NA	6.67E-06	mr1179	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
vg1214046223	NA	1.22E-06	mr1236	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
vg1214046223	2.35E-06	2.35E-06	mr1663	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
vg1214046223	9.42E-07	NA	mr1291_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
vg1214046223	1.89E-06	NA	mr1892_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