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Detailed information for vg0233648100:

Variant ID: vg0233648100 (JBrowse)	Variation Type: INDEL
Chromosome: chr02	Position: 33648100
Reference Allele: AGTGTTGTTAGGACAG	Alternative Allele: GGTGTTGTTAGGACAG,A
Primary Allele: GGTGTTGTTAGGACAG	Secondary Allele: AGTGTTGTTAGGACAG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGAAAACTTAAAAACAAATCGCAGCGGTAAAATTCAAACAGACCCGGAACTTCCTGGTAAGGAACTCCGGAACTTCCGGCCTGCCAGGCCCGGAACTTCC[AGTGTTGTTAGGACAG/GGTGTTGTTAGGACAG,A]
GAACTTCCGGGTTACATAACAAGGATGAAAATCAAATTTCAAAACAGGAGACTAAGCCAATCTTCACAAGATGATGCACAGGTATTCTAAGCAGGGGATA

Reverse complement sequence

TATCCCCTGCTTAGAATACCTGTGCATCATCTTGTGAAGATTGGCTTAGTCTCCTGTTTTGAAATTTGATTTTCATCCTTGTTATGTAACCCGGAAGTTC[CTGTCCTAACAACACT/CTGTCCTAACAACACC,T]
GGAAGTTCCGGGCCTGGCAGGCCGGAAGTTCCGGAGTTCCTTACCAGGAAGTTCCGGGTCTGTTTGAATTTTACCGCTGCGATTTGTTTTTAAGTTTTCA

Allele Frequencies:

Populations	Population Size	Frequency of GGTGTTGTTAGGACAG(primary allele)	Frequency of AGTGTTGTTAGGACAG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.00%	24.00%	0.99%	0.00%	NA
All Indica	2759	99.20%	0.80%	0.04%	0.00%	NA
All Japonica	1512	25.60%	71.50%	2.91%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	99.10%	0.80%	0.13%	0.00%	NA
Temperate Japonica	767	19.80%	75.60%	4.56%	0.00%	NA
Tropical Japonica	504	16.50%	83.30%	0.20%	0.00%	NA
Japonica Intermediate	241	63.10%	33.60%	3.32%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	65.60%	32.20%	2.22%	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
vg0233648100	AGTGTTGTTAGGACAG -> A	LOC_Os02g54940.1	upstream_gene_variant ; 2578.0bp to feature; MODIFIER	N	Average:36.954; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N
vg0233648100	AGTGTTGTTAGGACAG -> A	LOC_Os02g54930.1	downstream_gene_variant ; 3793.0bp to feature; MODIFIER	N	Average:36.954; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N
vg0233648100	AGTGTTGTTAGGACAG -> A	LOC_Os02g54930-LOC_Os02g54940	intergenic_region ; MODIFIER	N	Average:36.954; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N
vg0233648100	AGTGTTGTTAGGACAG -> GGTGTTGTTAGGACAG	LOC_Os02g54940.1	upstream_gene_variant ; 2579.0bp to feature; MODIFIER	silent_mutation	Average:36.954; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N
vg0233648100	AGTGTTGTTAGGACAG -> GGTGTTGTTAGGACAG	LOC_Os02g54930.1	downstream_gene_variant ; 3792.0bp to feature; MODIFIER	silent_mutation	Average:36.954; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N
vg0233648100	AGTGTTGTTAGGACAG -> GGTGTTGTTAGGACAG	LOC_Os02g54930-LOC_Os02g54940	intergenic_region ; MODIFIER	silent_mutation	Average:36.954; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0233648100	NA	1.91E-06	mr1510	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
vg0233648100	NA	5.63E-20	mr1010_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
vg0233648100	NA	4.97E-13	mr1035_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
vg0233648100	6.97E-07	NA	mr1071_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
vg0233648100	NA	1.26E-08	mr1071_2	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
vg0233648100	NA	3.29E-08	mr1080_2	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
vg0233648100	6.52E-06	NA	mr1100_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
vg0233648100	NA	2.16E-08	mr1100_2	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
vg0233648100	NA	3.27E-34	mr1137_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
vg0233648100	7.31E-09	NA	mr1203_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
vg0233648100	NA	5.30E-10	mr1203_2	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
vg0233648100	NA	3.92E-08	mr1613_2	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
vg0233648100	NA	1.17E-28	mr1617_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
vg0233648100	NA	3.27E-07	mr1619_2	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
vg0233648100	NA	1.34E-08	mr1913_2	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