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Detailed information for vg0609864337:

Variant ID: vg0609864337 (JBrowse)	Variation Type: INDEL
Chromosome: chr06	Position: 9864337
Reference Allele: AACCGTTT	Alternative Allele: CACCGTTT,A,ATGCACCGTTT,AATGCACCGTTT
Primary Allele: AACCGTTT	Secondary Allele: ATGCACCGTTT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGCTCATGATTAATTGAGTATTAACTATTTTAAATTTCAAAAATGGATTAATATGATTTTTTAAAGCAACTTTCCTATAAAAAATTTTTACAAAAAACG[AACCGTTT/CACCGTTT,A,ATGCACCGTTT,AATGCACCGTTT]
AGTAGTTTGGTAGTTTAGGAAACGTGTGCGCGGAAAACGAAACAAACAAACTCACTCTCTCACCCTCTCGAACGCTGCCTAAGTCATCACTAAGATTGTT

Reverse complement sequence

AACAATCTTAGTGATGACTTAGGCAGCGTTCGAGAGGGTGAGAGAGTGAGTTTGTTTGTTTCGTTTTCCGCGCACACGTTTCCTAAACTACCAAACTACT[AAACGGTT/AAACGGTG,T,AAACGGTGCAT,AAACGGTGCATT]
CGTTTTTTGTAAAAATTTTTTATAGGAAAGTTGCTTTAAAAAATCATATTAATCCATTTTTGAAATTTAAAATAGTTAATACTCAATTAATCATGAGCTA

Allele Frequencies:

Populations	Population Size	Frequency of AACCGTTT(primary allele)	Frequency of ATGCACCGTTT(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.90%	30.30%	0.63%	0.00%	A: 0.99%; AATGCACCGTTT: 0.11%; CACCGTTT: 0.08%
All Indica	2759	85.90%	13.90%	0.11%	0.00%	A: 0.14%
All Japonica	1512	51.10%	47.20%	1.26%	0.00%	AATGCACCGTTT: 0.33%; CACCGTTT: 0.13%
Aus	269	1.10%	81.80%	2.23%	0.00%	A: 14.87%
Indica I	595	99.20%	0.80%	0.00%	0.00%	NA
Indica II	465	83.20%	16.60%	0.22%	0.00%	NA
Indica III	913	81.70%	18.20%	0.11%	0.00%	NA
Indica Intermediate	786	82.20%	17.20%	0.13%	0.00%	A: 0.51%
Temperate Japonica	767	70.10%	29.20%	0.65%	0.00%	NA
Tropical Japonica	504	34.90%	61.70%	2.18%	0.00%	AATGCACCGTTT: 0.99%; CACCGTTT: 0.20%
Japonica Intermediate	241	24.10%	74.30%	1.24%	0.00%	CACCGTTT: 0.41%
VI/Aromatic	96	6.20%	87.50%	2.08%	0.00%	CACCGTTT: 2.08%; A: 2.08%
Intermediate	90	66.70%	32.20%	0.00%	0.00%	A: 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
vg0609864337	AACCGTTT -> CACCGTTT	LOC_Os06g17000.1	upstream_gene_variant ; 399.0bp to feature; MODIFIER	silent_mutation	Average:46.172; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0609864337	AACCGTTT -> CACCGTTT	LOC_Os06g17000-LOC_Os06g17020	intergenic_region ; MODIFIER	silent_mutation	Average:46.172; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0609864337	AACCGTTT -> A	LOC_Os06g17000.1	upstream_gene_variant ; 400.0bp to feature; MODIFIER	silent_mutation	Average:46.172; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0609864337	AACCGTTT -> A	LOC_Os06g17000-LOC_Os06g17020	intergenic_region ; MODIFIER	silent_mutation	Average:46.172; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0609864337	AACCGTTT -> ATGCACCGTTT	LOC_Os06g17000.1	upstream_gene_variant ; 400.0bp to feature; MODIFIER	silent_mutation	Average:46.172; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0609864337	AACCGTTT -> ATGCACCGTTT	LOC_Os06g17000-LOC_Os06g17020	intergenic_region ; MODIFIER	silent_mutation	Average:46.172; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0609864337	AACCGTTT -> AATGCACCGTTT	LOC_Os06g17000.1	upstream_gene_variant ; 401.0bp to feature; MODIFIER	silent_mutation	Average:46.172; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0609864337	AACCGTTT -> AATGCACCGTTT	LOC_Os06g17000-LOC_Os06g17020	intergenic_region ; MODIFIER	silent_mutation	Average:46.172; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0609864337	NA	2.61E-09	mr1090	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
vg0609864337	NA	1.69E-06	mr1121	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
vg0609864337	1.20E-06	4.41E-10	mr1211	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
vg0609864337	NA	7.34E-06	mr1535	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
vg0609864337	NA	6.00E-06	mr1004_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
vg0609864337	1.83E-06	1.42E-08	mr1090_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
vg0609864337	NA	4.85E-06	mr1121_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
vg0609864337	1.18E-06	8.99E-10	mr1211_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
vg0609864337	2.99E-08	NA	mr1571_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
vg0609864337	1.20E-06	1.20E-06	mr1571_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