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Detailed information for vg0123593589:

Variant ID: vg0123593589 (JBrowse)	Variation Type: INDEL
Chromosome: chr01	Position: 23593589
Reference Allele: CTAGCATTTCTCACATTCATATTGATGTTAATGAATGTAAATAGATATATATGTCTA	Alternative Allele: TTAGCATTTCTCACATTCATATTGATGTTAATGAATGTAAATAGATATATATGTCTA,C
Primary Allele: CTAGCATTTCTCACATTCAT ATTGATGTTAATGAATGTAA ATAGATATATATGTCTA	Secondary Allele: TTAGCATTTCTCACATTCAT ATTGATGTTAATGAATGTAA ATAGATATATATGTCTA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACCTTGTCGATATCTTCTTGCTTCTCCTGCCAATTTATCCTGTAATCATTTGTCTTCCTTGGTATCTACTACTTCCTCCGTTTCACAATGTAAGTCATT[CTAGCATTTCTCACATTCATATTGATGTTAATGAATGTAAATAGATATATATGTCTA/TTAGCATTTCTCACATTCATATTGATGTTAATGAATGTAAATAGATATATATGTCTA,C]
GATTCATTAATATCAATATGAATGTGAGAAATGTTAGAATGACTTACATTGTGAAACGAAGGGAATAGTATTTAACACAGCTAGTAGCTATAGGCCCTAT

Reverse complement sequence

ATAGGGCCTATAGCTACTAGCTGTGTTAAATACTATTCCCTTCGTTTCACAATGTAAGTCATTCTAACATTTCTCACATTCATATTGATATTAATGAATC[TAGACATATATATCTATTTACATTCATTAACATCAATATGAATGTGAGAAATGCTAG/TAGACATATATATCTATTTACATTCATTAACATCAATATGAATGTGAGAAATGCTAA,G]
AATGACTTACATTGTGAAACGGAGGAAGTAGTAGATACCAAGGAAGACAAATGATTACAGGATAAATTGGCAGGAGAAGCAAGAAGATATCGACAAGGTA

Allele Frequencies:

Populations	Population Size	Frequency of CTAGCATTTCTCACATTCAT ATTGATGTTAATGAATGTAA ATAGATATATATGTCTA(primary allele)	Frequency of TTAGCATTTCTCACATTCAT ATTGATGTTAATGAATGTAA ATAGATATATATGTCTA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.60%	25.70%	0.85%	0.85%	C: 8.06%
All Indica	2759	51.60%	37.30%	1.27%	1.01%	C: 8.81%
All Japonica	1512	83.80%	9.80%	0.13%	0.00%	C: 6.28%
Aus	269	92.60%	2.20%	0.00%	4.46%	C: 0.74%
Indica I	595	88.40%	4.20%	2.52%	0.00%	C: 4.87%
Indica II	465	58.50%	37.60%	1.29%	0.65%	C: 1.94%
Indica III	913	24.10%	56.50%	0.44%	1.64%	C: 17.31%
Indica Intermediate	786	51.50%	39.90%	1.27%	1.27%	C: 5.98%
Temperate Japonica	767	98.30%	0.80%	0.13%	0.00%	C: 0.78%
Tropical Japonica	504	62.70%	24.00%	0.00%	0.00%	C: 13.29%
Japonica Intermediate	241	81.70%	8.70%	0.41%	0.00%	C: 9.13%
VI/Aromatic	96	63.50%	2.10%	0.00%	0.00%	C: 34.38%
Intermediate	90	57.80%	30.00%	3.33%	0.00%	C: 8.89%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0123593589	CTAGCATTTCTCACATTCATATTGATGTTAATGAATGTAAATAGATATATATGTCTA -> DEL	N	N	silent_mutation	Average:73.72; most accessible tissue: Zhenshan97 flag leaf, score: 86.342	N	N	N	N
vg0123593589	CTAGCATTTCTCACATTCATATTGATGTTAATGAATGTAAATAGATATATATGTCTA -> C	LOC_Os01g41670.1	upstream_gene_variant ; 4712.0bp to feature; MODIFIER	silent_mutation	Average:73.72; most accessible tissue: Zhenshan97 flag leaf, score: 86.342	N	N	N	N
vg0123593589	CTAGCATTTCTCACATTCATATTGATGTTAATGAATGTAAATAGATATATATGTCTA -> C	LOC_Os01g41680.1	upstream_gene_variant ; 784.0bp to feature; MODIFIER	silent_mutation	Average:73.72; most accessible tissue: Zhenshan97 flag leaf, score: 86.342	N	N	N	N
vg0123593589	CTAGCATTTCTCACATTCATATTGATGTTAATGAATGTAAATAGATATATATGTCTA -> C	LOC_Os01g41690.1	upstream_gene_variant ; 1460.0bp to feature; MODIFIER	silent_mutation	Average:73.72; most accessible tissue: Zhenshan97 flag leaf, score: 86.342	N	N	N	N
vg0123593589	CTAGCATTTCTCACATTCATATTGATGTTAATGAATGTAAATAGATATATATGTCTA -> C	LOC_Os01g41680-LOC_Os01g41690	intergenic_region ; MODIFIER	silent_mutation	Average:73.72; most accessible tissue: Zhenshan97 flag leaf, score: 86.342	N	N	N	N
vg0123593589	CTAGCATTTCTCACATTCATATTGATGTTAATGAATGTAAATAGATATATATGTCTA -> TTAGCATTTCTCACATTCATATTGATGTTA ATGAATGTAAATAGATATATATGTCTA	LOC_Os01g41670.1	upstream_gene_variant ; 4711.0bp to feature; MODIFIER	silent_mutation	Average:73.72; most accessible tissue: Zhenshan97 flag leaf, score: 86.342	N	N	N	N
vg0123593589	CTAGCATTTCTCACATTCATATTGATGTTAATGAATGTAAATAGATATATATGTCTA -> TTAGCATTTCTCACATTCATATTGATGTTA ATGAATGTAAATAGATATATATGTCTA	LOC_Os01g41680.1	upstream_gene_variant ; 783.0bp to feature; MODIFIER	silent_mutation	Average:73.72; most accessible tissue: Zhenshan97 flag leaf, score: 86.342	N	N	N	N
vg0123593589	CTAGCATTTCTCACATTCATATTGATGTTAATGAATGTAAATAGATATATATGTCTA -> TTAGCATTTCTCACATTCATATTGATGTTA ATGAATGTAAATAGATATATATGTCTA	LOC_Os01g41690.1	upstream_gene_variant ; 1461.0bp to feature; MODIFIER	silent_mutation	Average:73.72; most accessible tissue: Zhenshan97 flag leaf, score: 86.342	N	N	N	N
vg0123593589	CTAGCATTTCTCACATTCATATTGATGTTAATGAATGTAAATAGATATATATGTCTA -> TTAGCATTTCTCACATTCATATTGATGTTA ATGAATGTAAATAGATATATATGTCTA	LOC_Os01g41680-LOC_Os01g41690	intergenic_region ; MODIFIER	silent_mutation	Average:73.72; most accessible tissue: Zhenshan97 flag leaf, score: 86.342	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0123593589	NA	5.75E-06	mr1072	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
vg0123593589	4.33E-06	4.51E-06	mr1346	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
vg0123593589	5.31E-06	2.42E-06	mr1456	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
vg0123593589	NA	2.61E-07	mr1561	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
vg0123593589	NA	1.60E-06	mr1561	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
vg0123593589	NA	1.36E-07	mr1587	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
vg0123593589	NA	9.89E-06	mr1780	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
vg0123593589	NA	2.79E-07	mr1861	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
vg0123593589	NA	1.86E-06	mr1875	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
vg0123593589	NA	7.30E-08	mr1908	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
vg0123593589	NA	7.22E-06	mr1908	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
vg0123593589	NA	2.26E-07	mr1072_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
vg0123593589	NA	3.40E-08	mr1124_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
vg0123593589	NA	1.29E-09	mr1380_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
vg0123593589	NA	1.06E-09	mr1380_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
vg0123593589	NA	9.75E-07	mr1422_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
vg0123593589	NA	8.23E-07	mr1531_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
vg0123593589	NA	5.64E-11	mr1561_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
vg0123593589	NA	8.49E-10	mr1561_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
vg0123593589	NA	1.89E-07	mr1606_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
vg0123593589	NA	2.55E-06	mr1807_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
vg0123593589	NA	8.71E-09	mr1875_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
vg0123593589	NA	6.83E-07	mr1875_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
vg0123593589	NA	2.54E-10	mr1908_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
vg0123593589	NA	1.90E-08	mr1908_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
vg0123593589	NA	1.26E-08	mr1996_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
vg0123593589	NA	9.83E-09	mr1996_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