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Detailed information for vg1009141969:

Variant ID: vg1009141969 (JBrowse)	Variation Type: INDEL
Chromosome: chr10	Position: 9141969
Reference Allele: GGGACTAAAGACGGTTGGTGGCTACAACGGGCATATGT	Alternative Allele: AGGACTAAAGACGGTTGGTGGCTACAACGGGCATATGT,G
Primary Allele: GGGACTAAAGACGGTTGGTG GCTACAACGGGCATATGT	Secondary Allele: AGGACTAAAGACGGTTGGTG GCTACAACGGGCATATGT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACGGCCGCTCAAGCTGTATGCCACCAGCCTACACTGGTGGAGAAACCATCTTTGGTTGGTCGGCCGAAATCCACAATAGTCCTGGATCCATTTAAAACC[GGGACTAAAGACGGTTGGTGGCTACAACGGGCATATGT/AGGACTAAAGACGGTTGGTGGCTACAACGGGCATATGT,G]
GATCTTTAGTCCCGGTTGGTAATACCAACTGAGACTAAAGATCATCTTTAGTCCCGGTTGTAGAGATGTCAGACGTTGTCAGGGCCCCCGGGATCTTTAG

Reverse complement sequence

CTAAAGATCCCGGGGGCCCTGACAACGTCTGACATCTCTACAACCGGGACTAAAGATGATCTTTAGTCTCAGTTGGTATTACCAACCGGGACTAAAGATC[ACATATGCCCGTTGTAGCCACCAACCGTCTTTAGTCCC/ACATATGCCCGTTGTAGCCACCAACCGTCTTTAGTCCT,C]
GGTTTTAAATGGATCCAGGACTATTGTGGATTTCGGCCGACCAACCAAAGATGGTTTCTCCACCAGTGTAGGCTGGTGGCATACAGCTTGAGCGGCCGTC

Allele Frequencies:

Populations	Population Size	Frequency of GGGACTAAAGACGGTTGGTG GCTACAACGGGCATATGT(primary allele)	Frequency of AGGACTAAAGACGGTTGGTG GCTACAACGGGCATATGT(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.50%	26.60%	1.42%	0.51%	G: 0.04%
All Indica	2759	74.70%	22.80%	1.99%	0.51%	NA
All Japonica	1512	60.60%	38.20%	0.53%	0.66%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	98.30%	1.50%	0.17%	0.00%	NA
Indica II	465	77.20%	21.10%	1.51%	0.22%	NA
Indica III	913	55.00%	40.10%	3.72%	1.20%	NA
Indica Intermediate	786	78.20%	19.80%	1.65%	0.25%	NA
Temperate Japonica	767	89.20%	10.70%	0.00%	0.13%	NA
Tropical Japonica	504	16.70%	80.60%	1.59%	1.19%	NA
Japonica Intermediate	241	61.40%	37.30%	0.00%	1.24%	NA
VI/Aromatic	96	76.00%	24.00%	0.00%	0.00%	NA
Intermediate	90	67.80%	25.60%	4.44%	0.00%	G: 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
vg1009141969	GGGACTAAAGACGGTTGGTGGCTACAACGGGCATATGT -> DEL	N	N	silent_mutation	Average:54.309; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg1009141969	GGGACTAAAGACGGTTGGTGGCTACAACGGGCATATGT -> G	LOC_Os10g18010.1	upstream_gene_variant ; 2946.0bp to feature; MODIFIER	silent_mutation	Average:54.309; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg1009141969	GGGACTAAAGACGGTTGGTGGCTACAACGGGCATATGT -> G	LOC_Os10g18042.1	upstream_gene_variant ; 1839.0bp to feature; MODIFIER	silent_mutation	Average:54.309; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg1009141969	GGGACTAAAGACGGTTGGTGGCTACAACGGGCATATGT -> G	LOC_Os10g18026.1	intron_variant ; MODIFIER	silent_mutation	Average:54.309; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg1009141969	GGGACTAAAGACGGTTGGTGGCTACAACGGGCATATGT -> AGGACTAAAGACGGTTGGTGGCTACAACGG GCATATGT	LOC_Os10g18010.1	upstream_gene_variant ; 2945.0bp to feature; MODIFIER	silent_mutation	Average:54.309; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg1009141969	GGGACTAAAGACGGTTGGTGGCTACAACGGGCATATGT -> AGGACTAAAGACGGTTGGTGGCTACAACGG GCATATGT	LOC_Os10g18042.1	upstream_gene_variant ; 1840.0bp to feature; MODIFIER	silent_mutation	Average:54.309; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg1009141969	GGGACTAAAGACGGTTGGTGGCTACAACGGGCATATGT -> AGGACTAAAGACGGTTGGTGGCTACAACGG GCATATGT	LOC_Os10g18026.1	intron_variant ; MODIFIER	silent_mutation	Average:54.309; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009141969	6.76E-06	NA	mr1026	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
vg1009141969	NA	2.69E-12	mr1026	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
vg1009141969	9.83E-06	NA	mr1110	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
vg1009141969	3.50E-07	2.04E-11	mr1113	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
vg1009141969	9.45E-08	5.32E-11	mr1114	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
vg1009141969	1.23E-07	1.65E-11	mr1116	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
vg1009141969	8.37E-08	2.63E-29	mr1118	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
vg1009141969	4.13E-11	6.04E-22	mr1118	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
vg1009141969	NA	1.39E-06	mr1118	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
vg1009141969	NA	1.78E-08	mr1119	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
vg1009141969	NA	1.15E-07	mr1120	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
vg1009141969	NA	2.24E-11	mr1161	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
vg1009141969	NA	9.46E-09	mr1183	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
vg1009141969	9.69E-08	2.26E-11	mr1247	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
vg1009141969	NA	6.17E-06	mr1328	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
vg1009141969	7.47E-08	1.86E-32	mr1495	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
vg1009141969	8.44E-12	7.33E-25	mr1495	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
vg1009141969	NA	2.42E-07	mr1496	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
vg1009141969	NA	3.65E-08	mr1503	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
vg1009141969	4.98E-06	2.98E-11	mr1794	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
vg1009141969	NA	2.02E-06	mr1842	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
vg1009141969	NA	2.38E-07	mr1917	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
vg1009141969	NA	5.28E-06	mr1936	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
vg1009141969	NA	1.91E-10	mr1980	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
vg1009141969	1.95E-06	3.07E-12	mr1113_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
vg1009141969	6.58E-07	3.72E-13	mr1114_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
vg1009141969	9.00E-06	3.16E-10	mr1117_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
vg1009141969	NA	1.47E-23	mr1118_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
vg1009141969	3.64E-10	1.01E-21	mr1118_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
vg1009141969	NA	1.58E-09	mr1119_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
vg1009141969	1.26E-06	1.64E-13	mr1120_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
vg1009141969	9.31E-07	5.31E-12	mr1161_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
vg1009141969	1.76E-06	9.78E-13	mr1247_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
vg1009141969	1.17E-07	NA	mr1258_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
vg1009141969	5.77E-07	5.29E-09	mr1258_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
vg1009141969	NA	2.76E-06	mr1398_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
vg1009141969	1.63E-07	2.04E-29	mr1495_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
vg1009141969	1.08E-11	2.00E-24	mr1495_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
vg1009141969	3.26E-06	NA	mr1794_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
vg1009141969	5.38E-06	2.56E-15	mr1794_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
vg1009141969	NA	1.94E-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
vg1009141969	NA	4.19E-06	mr1961_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
vg1009141969	NA	1.83E-07	mr1991_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