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Detailed information for vg1000493003:

Variant ID: vg1000493003 (JBrowse)	Variation Type: INDEL
Chromosome: chr10	Position: 493003
Reference Allele: G	Alternative Allele: A,GA
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACCATATATAATACTCCCTCCGTATTTTAATGTATGACGCCGTTGACTATTCGACCAACGTTTGACCATTTGTTTTATTCAAAATTTTTATGCAAATAT[G/A,GA]
AAAATATTTATGTTATGCTTAAAGAACATTTGATGACGAATCAAGTTATAATAAAATAAATGATAATTACATAAATTTTTTGAATAAGACGAATGGTCAA

Reverse complement sequence

TTGACCATTCGTCTTATTCAAAAAATTTATGTAATTATCATTTATTTTATTATAACTTGATTCGTCATCAAATGTTCTTTAAGCATAACATAAATATTTT[C/T,TC]
ATATTTGCATAAAAATTTTGAATAAAACAAATGGTCAAACGTTGGTCGAATAGTCAACGGCGTCATACATTAAAATACGGAGGGAGTATTATATATGGTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.00%	5.10%	0.76%	6.12%	GA: 0.06%
All Indica	2759	95.70%	0.70%	0.40%	3.23%	GA: 0.04%
All Japonica	1512	93.50%	6.00%	0.00%	0.53%	NA
Aus	269	6.70%	31.20%	8.18%	53.53%	GA: 0.37%
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.10%	0.20%	0.00%	0.65%	NA
Indica III	913	93.80%	0.20%	0.55%	5.48%	NA
Indica Intermediate	786	92.60%	1.90%	0.76%	4.58%	GA: 0.13%
Temperate Japonica	767	91.40%	8.50%	0.00%	0.13%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	87.60%	9.50%	0.00%	2.90%	NA
VI/Aromatic	96	15.60%	41.70%	2.08%	40.62%	NA
Intermediate	90	80.00%	7.80%	1.11%	10.00%	GA: 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
vg1000493003	G -> GA	LOC_Os10g01760.1	upstream_gene_variant ; 3532.0bp to feature; MODIFIER	silent_mutation	Average:45.078; most accessible tissue: Minghui63 root, score: 68.289	N	N	N	N
vg1000493003	G -> GA	LOC_Os10g01760-LOC_Os10g01770	intergenic_region ; MODIFIER	silent_mutation	Average:45.078; most accessible tissue: Minghui63 root, score: 68.289	N	N	N	N
vg1000493003	G -> A	LOC_Os10g01760.1	upstream_gene_variant ; 3531.0bp to feature; MODIFIER	silent_mutation	Average:45.078; most accessible tissue: Minghui63 root, score: 68.289	N	N	N	N
vg1000493003	G -> A	LOC_Os10g01760-LOC_Os10g01770	intergenic_region ; MODIFIER	silent_mutation	Average:45.078; most accessible tissue: Minghui63 root, score: 68.289	N	N	N	N
vg1000493003	G -> DEL	N	N	silent_mutation	Average:45.078; most accessible tissue: Minghui63 root, score: 68.289	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000493003	NA	1.41E-07	mr1040	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
vg1000493003	1.55E-07	NA	mr1310	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
vg1000493003	2.01E-06	NA	mr1549	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
vg1000493003	NA	2.47E-08	mr1549	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
vg1000493003	NA	2.92E-06	mr1550	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
vg1000493003	1.64E-09	NA	mr1757	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
vg1000493003	6.66E-07	1.48E-11	mr1757	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
vg1000493003	2.00E-08	NA	mr1926	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
vg1000493003	NA	2.38E-07	mr1968	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
vg1000493003	5.57E-13	NA	mr1310_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
vg1000493003	5.88E-09	NA	mr1310_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
vg1000493003	NA	2.61E-08	mr1549_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
vg1000493003	NA	1.41E-06	mr1550_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
vg1000493003	5.88E-07	NA	mr1757_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
vg1000493003	NA	2.29E-08	mr1757_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
vg1000493003	9.12E-07	NA	mr1959_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
vg1000493003	NA	1.81E-08	mr1968_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