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Detailed information for vg1222399385:

Variant ID: vg1222399385 (JBrowse)	Variation Type: INDEL
Chromosome: chr12	Position: 22399385
Reference Allele: C	Alternative Allele: T,CCTCTAATTAATCTAGTTTAACTGGCGACAGGGGTTTGGG,CCTCTAATTAATCTAGTTTAACTGGCGACGGGTTTGGG
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATCAATTTTCATCATGCAATAATTGTAAATCCAGTGATAGTTTTTAAAGAAATGATTTGAAATGTTTTTATGAAATATAGAAGAAATACAATAAATTCA[C/T,CCTCTAATTAATCTAGTTTAACTGGCGACAGGGGTTTGGG,CCTCTAATTAATCTAGTTTAACTGGCGACGGGTTTGGG]
ATGCAATAATTTTACCGTCCTTGAGAAGGTACCATGAGGTACCACTTATGCTACCTTCCAAATGACTGTAAAATTGCCCAATTCTAGCAACAGGAGCAAA

Reverse complement sequence

TTTGCTCCTGTTGCTAGAATTGGGCAATTTTACAGTCATTTGGAAGGTAGCATAAGTGGTACCTCATGGTACCTTCTCAAGGACGGTAAAATTATTGCAT[G/A,CCCAAACCCCTGTCGCCAGTTAAACTAGATTAATTAGAGG,CCCAAACCCGTCGCCAGTTAAACTAGATTAATTAGAGG]
TGAATTTATTGTATTTCTTCTATATTTCATAAAAACATTTCAAATCATTTCTTTAAAAACTATCACTGGATTTACAATTATTGCATGATGAAAATTGATA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.10%	10.10%	18.73%	9.56%	CCTCTAATTAATCTAGTTTAACTGGCGACAGGGGTTTGGG: 5.27%; CCTCTAATTAATCTAGTTTAACTGGCGACGGGTTTGGG: 0.23%
All Indica	2759	39.00%	14.50%	24.61%	14.35%	CCTCTAATTAATCTAGTTTAACTGGCGACAGGGGTTTGGG: 7.39%; CCTCTAATTAATCTAGTTTAACTGGCGACGGGTTTGGG: 0.11%
All Japonica	1512	86.80%	2.50%	7.54%	1.98%	CCTCTAATTAATCTAGTTTAACTGGCGACAGGGGTTTGGG: 1.19%
Aus	269	36.80%	13.80%	29.00%	8.92%	CCTCTAATTAATCTAGTTTAACTGGCGACAGGGGTTTGGG: 8.55%; CCTCTAATTAATCTAGTTTAACTGGCGACGGGTTTGGG: 2.97%
Indica I	595	39.80%	13.10%	32.94%	11.60%	CCTCTAATTAATCTAGTTTAACTGGCGACAGGGGTTTGGG: 2.52%
Indica II	465	22.40%	14.40%	27.74%	32.04%	CCTCTAATTAATCTAGTTTAACTGGCGACAGGGGTTTGGG: 3.44%
Indica III	913	44.90%	16.40%	18.51%	7.67%	CCTCTAATTAATCTAGTTTAACTGGCGACAGGGGTTTGGG: 12.27%; CCTCTAATTAATCTAGTTTAACTGGCGACGGGTTTGGG: 0.22%
Indica Intermediate	786	41.30%	13.50%	23.54%	13.74%	CCTCTAATTAATCTAGTTTAACTGGCGACAGGGGTTTGGG: 7.76%; CCTCTAATTAATCTAGTTTAACTGGCGACGGGTTTGGG: 0.13%
Temperate Japonica	767	91.50%	1.20%	5.74%	1.30%	CCTCTAATTAATCTAGTTTAACTGGCGACAGGGGTTTGGG: 0.26%
Tropical Japonica	504	78.60%	5.20%	10.12%	3.37%	CCTCTAATTAATCTAGTTTAACTGGCGACAGGGGTTTGGG: 2.78%
Japonica Intermediate	241	88.80%	1.20%	7.88%	1.24%	CCTCTAATTAATCTAGTTTAACTGGCGACAGGGGTTTGGG: 0.83%
VI/Aromatic	96	94.80%	0.00%	3.12%	0.00%	CCTCTAATTAATCTAGTTTAACTGGCGACAGGGGTTTGGG: 2.08%
Intermediate	90	80.00%	3.30%	12.22%	2.22%	CCTCTAATTAATCTAGTTTAACTGGCGACAGGGGTTTGGG: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1222399385	C -> CCTCTAATTAATCTAGTTTAACTGGCGACA GGGGTTTGGG	LOC_Os12g36590.1	upstream_gene_variant ; 4431.0bp to feature; MODIFIER	silent_mutation	Average:18.568; most accessible tissue: Callus, score: 34.927	N	N	N	N
vg1222399385	C -> CCTCTAATTAATCTAGTTTAACTGGCGACA GGGGTTTGGG	LOC_Os12g36580.1	downstream_gene_variant ; 2003.0bp to feature; MODIFIER	silent_mutation	Average:18.568; most accessible tissue: Callus, score: 34.927	N	N	N	N
vg1222399385	C -> CCTCTAATTAATCTAGTTTAACTGGCGACA GGGGTTTGGG	LOC_Os12g36580-LOC_Os12g36590	intergenic_region ; MODIFIER	silent_mutation	Average:18.568; most accessible tissue: Callus, score: 34.927	N	N	N	N
vg1222399385	C -> CCTCTAATTAATCTAGTTTAACTGGCGACG GGTTTGGG	LOC_Os12g36590.1	upstream_gene_variant ; 4431.0bp to feature; MODIFIER	silent_mutation	Average:18.568; most accessible tissue: Callus, score: 34.927	N	N	N	N
vg1222399385	C -> CCTCTAATTAATCTAGTTTAACTGGCGACG GGTTTGGG	LOC_Os12g36580.1	downstream_gene_variant ; 2003.0bp to feature; MODIFIER	silent_mutation	Average:18.568; most accessible tissue: Callus, score: 34.927	N	N	N	N
vg1222399385	C -> CCTCTAATTAATCTAGTTTAACTGGCGACG GGTTTGGG	LOC_Os12g36580-LOC_Os12g36590	intergenic_region ; MODIFIER	silent_mutation	Average:18.568; most accessible tissue: Callus, score: 34.927	N	N	N	N
vg1222399385	C -> DEL	N	N	silent_mutation	Average:18.568; most accessible tissue: Callus, score: 34.927	N	N	N	N
vg1222399385	C -> T	LOC_Os12g36590.1	upstream_gene_variant ; 4432.0bp to feature; MODIFIER	silent_mutation	Average:18.568; most accessible tissue: Callus, score: 34.927	N	N	N	N
vg1222399385	C -> T	LOC_Os12g36580.1	downstream_gene_variant ; 2002.0bp to feature; MODIFIER	silent_mutation	Average:18.568; most accessible tissue: Callus, score: 34.927	N	N	N	N
vg1222399385	C -> T	LOC_Os12g36580-LOC_Os12g36590	intergenic_region ; MODIFIER	silent_mutation	Average:18.568; most accessible tissue: Callus, score: 34.927	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222399385	NA	2.59E-08	mr1013	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
vg1222399385	NA	1.72E-07	mr1015	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
vg1222399385	NA	5.59E-08	mr1021	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
vg1222399385	NA	3.14E-09	mr1031	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
vg1222399385	NA	3.17E-07	mr1032	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
vg1222399385	NA	4.54E-06	mr1034	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
vg1222399385	NA	4.45E-08	mr1056	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
vg1222399385	NA	6.42E-06	mr1127	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
vg1222399385	5.24E-06	5.26E-06	mr1160	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
vg1222399385	NA	2.57E-07	mr1162	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
vg1222399385	NA	9.88E-07	mr1165	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
vg1222399385	NA	3.39E-06	mr1285	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
vg1222399385	NA	1.52E-06	mr1291	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
vg1222399385	NA	3.78E-06	mr1291	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
vg1222399385	NA	7.41E-06	mr1324	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
vg1222399385	NA	3.57E-06	mr1344	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
vg1222399385	NA	9.71E-06	mr1398	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
vg1222399385	NA	9.28E-09	mr1477	Ind_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
vg1222399385	NA	4.44E-07	mr1478	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
vg1222399385	NA	9.86E-07	mr1513	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
vg1222399385	NA	2.55E-07	mr1590	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
vg1222399385	NA	2.39E-06	mr1660	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
vg1222399385	NA	9.88E-06	mr1783	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
vg1222399385	NA	6.42E-06	mr1964	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
vg1222399385	NA	1.82E-06	mr1965	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
vg1222399385	NA	2.08E-06	mr1981	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
vg1222399385	NA	3.25E-06	mr1041_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
vg1222399385	NA	8.07E-07	mr1184_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
vg1222399385	NA	6.73E-06	mr1278_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
vg1222399385	NA	2.34E-07	mr1293_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
vg1222399385	NA	5.72E-06	mr1497_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
vg1222399385	NA	2.18E-06	mr1508_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
vg1222399385	NA	2.73E-08	mr1604_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
vg1222399385	NA	2.32E-07	mr1683_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
vg1222399385	7.18E-06	2.94E-08	mr1706_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
vg1222399385	NA	3.29E-06	mr1706_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