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Detailed information for vg0817495758:

Variant ID: vg0817495758 (JBrowse)	Variation Type: INDEL
Chromosome: chr08	Position: 17495758
Reference Allele: T	Alternative Allele: C,TAAATGTGCTC
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCCATCTCAATCGGCTTCTCGGAAATTGCATTATAAGGCTTTGAAGTACACCTTGTTGGATGATGAGTTATATTATCGAACGATTGATGGGGTGTTGCT[T/C,TAAATGTGCTC]
AAGTGTTTGAGTGCCGATCAAGCCAAAATTGCGATAGGCAAGGTAAATGAAGGAATTTGTGGTACTCATCAATCGGCTCACAAGATGAAGTGGTTACTTC

Reverse complement sequence

GAAGTAACCACTTCATCTTGTGAGCCGATTGATGAGTACCACAAATTCCTTCATTTACCTTGCCTATCGCAATTTTGGCTTGATCGGCACTCAAACACTT[A/G,GAGCACATTTA]
AGCAACACCCCATCAATCGTTCGATAATATAACTCATCATCCAACAAGGTGTACTTCAAAGCCTTATAATGCAATTTCCGAGAAGCCGATTGAGATGGAT

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	82.80%	0.60%	3.55%	13.01%	NA
All Indica	2759	78.70%	1.00%	4.24%	16.02%	NA
All Japonica	1512	88.60%	0.00%	2.84%	8.60%	NA
Aus	269	87.70%	0.00%	2.23%	10.04%	NA
Indica I	595	95.50%	0.30%	0.84%	3.36%	NA
Indica II	465	85.80%	0.90%	3.44%	9.89%	NA
Indica III	913	65.30%	1.30%	6.24%	27.16%	NA
Indica Intermediate	786	77.50%	1.30%	4.96%	16.28%	NA
Temperate Japonica	767	99.00%	0.00%	0.26%	0.78%	NA
Tropical Japonica	504	70.80%	0.00%	7.34%	21.83%	NA
Japonica Intermediate	241	92.50%	0.00%	1.66%	5.81%	NA
VI/Aromatic	96	94.80%	0.00%	0.00%	5.21%	NA
Intermediate	90	85.60%	0.00%	2.22%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817495758	T -> C	LOC_Os08g28630.1	synonymous_variant ; p.Leu1140Leu; LOW	synonymous_codon	Average:16.025; most accessible tissue: Callus, score: 34.268	N	N	N	N
vg0817495758	T -> TAAATGTGCTC	LOC_Os08g28630.1	frameshift_variant ; p.Leu1143fs; HIGH	N	Average:16.025; most accessible tissue: Callus, score: 34.268	N	N	N	N
vg0817495758	T -> TAAATGTGCTC	LOC_Os08g28650.1	upstream_gene_variant ; 4698.0bp to feature; MODIFIER	N	Average:16.025; most accessible tissue: Callus, score: 34.268	N	N	N	N
vg0817495758	T -> DEL	LOC_Os08g28630.1	N	frameshift_variant	Average:16.025; most accessible tissue: Callus, score: 34.268	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817495758	NA	1.42E-06	mr1133_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
vg0817495758	1.14E-06	6.07E-08	mr1667_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