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Detailed information for vg1209677354:

Variant ID: vg1209677354 (JBrowse)	Variation Type: INDEL
Chromosome: chr12	Position: 9677354
Reference Allele: TTA	Alternative Allele: CTA,T,TGTA,TGTCACGACCGGAAATA
Primary Allele: TTA	Secondary Allele: CTA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAATCAATCAACCTCAGTTGAAGAAAATGATCCAGAAGGAGAAGACGTTTGGCTTATACCCCAGTTGAGCTGCCTGTGGGAGTGGAGCTTAAGCCATCG[TTA/CTA,T,TGTA,TGTCACGACCGGAAATA]
GACCGTTAATTCCGCTGCTGTTTTTCTATTCTTTTGTAAGTATGTAACGATGTTATTATAATGGATTTGTATATAAAATCCTCGGCTGATTCCTGGACGA

Reverse complement sequence

TCGTCCAGGAATCAGCCGAGGATTTTATATACAAATCCATTATAATAACATCGTTACATACTTACAAAAGAATAGAAAAACAGCAGCGGAATTAACGGTC[TAA/TAG,A,TACA,TATTTCCGGTCGTGACA]
CGATGGCTTAAGCTCCACTCCCACAGGCAGCTCAACTGGGGTATAAGCCAAACGTCTTCTCCTTCTGGATCATTTTCTTCAACTGAGGTTGATTGATTAT

Allele Frequencies:

Populations	Population Size	Frequency of TTA(primary allele)	Frequency of CTA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	36.90%	14.60%	19.45%	26.77%	TGTA: 1.40%; T: 0.61%; TGTCACGACCGGAAATA: 0.34%
All Indica	2759	20.20%	19.30%	17.65%	40.52%	TGTA: 1.27%; T: 0.65%; TGTCACGACCGGAAATA: 0.36%
All Japonica	1512	74.30%	6.90%	12.50%	4.89%	TGTA: 0.73%; T: 0.53%; TGTCACGACCGGAAATA: 0.13%
Aus	269	3.00%	10.00%	63.94%	16.73%	TGTA: 4.46%; TGTCACGACCGGAAATA: 1.12%; T: 0.74%
Indica I	595	29.20%	12.10%	35.13%	20.00%	TGTA: 1.85%; T: 1.34%; TGTCACGACCGGAAATA: 0.34%
Indica II	465	30.50%	32.30%	5.81%	30.54%	TGTA: 0.86%
Indica III	913	7.00%	15.20%	12.60%	63.86%	TGTA: 0.66%; T: 0.33%; TGTCACGACCGGAAATA: 0.33%
Indica Intermediate	786	22.60%	21.90%	17.30%	34.86%	TGTA: 1.78%; T: 0.89%; TGTCACGACCGGAAATA: 0.64%
Temperate Japonica	767	85.10%	3.30%	4.95%	6.13%	T: 0.26%; TGTA: 0.26%
Tropical Japonica	504	66.70%	9.70%	18.06%	4.76%	TGTA: 0.60%; TGTCACGACCGGAAATA: 0.20%
Japonica Intermediate	241	55.60%	12.90%	24.90%	1.24%	T: 2.49%; TGTA: 2.49%; TGTCACGACCGGAAATA: 0.41%
VI/Aromatic	96	11.50%	11.50%	47.92%	21.88%	TGTA: 5.21%; TGTCACGACCGGAAATA: 1.04%; T: 1.04%
Intermediate	90	47.80%	13.30%	27.78%	7.78%	TGTA: 3.33%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1209677354	TTA -> T	LOC_Os12g16870.1	upstream_gene_variant ; 1740.0bp to feature; MODIFIER	silent_mutation	Average:46.999; most accessible tissue: Minghui63 flag leaf, score: 77.494	N	N	N	N
vg1209677354	TTA -> T	LOC_Os12g16870-LOC_Os12g16880	intergenic_region ; MODIFIER	silent_mutation	Average:46.999; most accessible tissue: Minghui63 flag leaf, score: 77.494	N	N	N	N
vg1209677354	TTA -> TGTA	LOC_Os12g16870.1	upstream_gene_variant ; 1740.0bp to feature; MODIFIER	silent_mutation	Average:46.999; most accessible tissue: Minghui63 flag leaf, score: 77.494	N	N	N	N
vg1209677354	TTA -> TGTA	LOC_Os12g16870-LOC_Os12g16880	intergenic_region ; MODIFIER	silent_mutation	Average:46.999; most accessible tissue: Minghui63 flag leaf, score: 77.494	N	N	N	N
vg1209677354	TTA -> DEL	N	N	silent_mutation	Average:46.999; most accessible tissue: Minghui63 flag leaf, score: 77.494	N	N	N	N
vg1209677354	TTA -> CTA	LOC_Os12g16870.1	upstream_gene_variant ; 1739.0bp to feature; MODIFIER	silent_mutation	Average:46.999; most accessible tissue: Minghui63 flag leaf, score: 77.494	N	N	N	N
vg1209677354	TTA -> CTA	LOC_Os12g16870-LOC_Os12g16880	intergenic_region ; MODIFIER	silent_mutation	Average:46.999; most accessible tissue: Minghui63 flag leaf, score: 77.494	N	N	N	N
vg1209677354	TTA -> TGTCACGACCGGAAATA	LOC_Os12g16870.1	upstream_gene_variant ; 1740.0bp to feature; MODIFIER	silent_mutation	Average:46.999; most accessible tissue: Minghui63 flag leaf, score: 77.494	N	N	N	N
vg1209677354	TTA -> TGTCACGACCGGAAATA	LOC_Os12g16870-LOC_Os12g16880	intergenic_region ; MODIFIER	silent_mutation	Average:46.999; most accessible tissue: Minghui63 flag leaf, score: 77.494	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209677354	1.22E-06	1.71E-07	mr1425	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
vg1209677354	4.20E-07	4.68E-10	mr1425	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
vg1209677354	NA	5.95E-08	mr1425_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
vg1209677354	NA	4.53E-07	mr1425_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