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Detailed information for vg0620976126:

Variant ID: vg0620976126 (JBrowse)	Variation Type: INDEL
Chromosome: chr06	Position: 20976126
Reference Allele: G	Alternative Allele: A,GTGGTTGAA
Primary Allele: G	Secondary Allele: GTGGTTGAA

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

GGGTTGTACCGGAGAAACCAGGTCAATACTTCTTCGATTGTTGTCACACTGTGAACTTTGAACTACTGACCAGGCTCAAACGGCTAGTCTGAGTGGTTGA[G/A,GTGGTTGAA]
GCTATATGTCTGACGCTAGCGAACGGGCCTCTAGCTGAGTTGGTTAGGTGGCTCTAGTAGCACTCTCAAGTCTTGAGTTCGACTCCCCATGTGAGTGAAT

Reverse complement sequence

ATTCACTCACATGGGGAGTCGAACTCAAGACTTGAGAGTGCTACTAGAGCCACCTAACCAACTCAGCTAGAGGCCCGTTCGCTAGCGTCAGACATATAGC[C/T,TTCAACCAC]
TCAACCACTCAGACTAGCCGTTTGAGCCTGGTCAGTAGTTCAAAGTTCACAGTGTGACAACAATCGAAGAAGTATTGACCTGGTTTCTCCGGTACAACCC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of GTGGTTGAA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.60%	14.60%	0.47%	0.15%	A: 0.17%
All Indica	2759	75.00%	23.70%	0.72%	0.22%	A: 0.29%
All Japonica	1512	99.10%	0.70%	0.07%	0.07%	NA
Aus	269	94.80%	4.80%	0.37%	0.00%	NA
Indica I	595	97.60%	2.20%	0.00%	0.00%	A: 0.17%
Indica II	465	69.70%	27.50%	2.80%	0.00%	NA
Indica III	913	56.70%	42.20%	0.33%	0.44%	A: 0.33%
Indica Intermediate	786	82.30%	16.40%	0.51%	0.25%	A: 0.51%
Temperate Japonica	767	98.70%	1.00%	0.13%	0.13%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0620976126	G -> A	LOC_Os06g35940.1	upstream_gene_variant ; 1893.0bp to feature; MODIFIER	silent_mutation	Average:57.069; most accessible tissue: Zhenshan97 young leaf, score: 81.6	N	N	N	N
vg0620976126	G -> A	LOC_Os06g35940-LOC_Os06g35950	intergenic_region ; MODIFIER	silent_mutation	Average:57.069; most accessible tissue: Zhenshan97 young leaf, score: 81.6	N	N	N	N
vg0620976126	G -> DEL	N	N	silent_mutation	Average:57.069; most accessible tissue: Zhenshan97 young leaf, score: 81.6	N	N	N	N
vg0620976126	G -> GTGGTTGAA	LOC_Os06g35940.1	upstream_gene_variant ; 1894.0bp to feature; MODIFIER	silent_mutation	Average:57.069; most accessible tissue: Zhenshan97 young leaf, score: 81.6	N	N	N	N
vg0620976126	G -> GTGGTTGAA	LOC_Os06g35940-LOC_Os06g35950	intergenic_region ; MODIFIER	silent_mutation	Average:57.069; most accessible tissue: Zhenshan97 young leaf, score: 81.6	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0620976126	6.63E-07	NA	mr1162_2	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
vg0620976126	NA	1.20E-06	mr1582_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
vg0620976126	NA	1.96E-06	mr1734_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