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Detailed information for vg0818051811:

Variant ID: vg0818051811 (JBrowse)	Variation Type: INDEL
Chromosome: chr08	Position: 18051811
Reference Allele: G	Alternative Allele: GTGCGTTGCCGAGCCGCAGCCGGTGATGACATCATTGC,A,C
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTACTATAAACATCCATTTCACAGTGGTACACCTCTGGCTAGAGTAAAACTATTCGAATAGCCGTGCCCGCGGTTATGGGTGGGTCTAACAATGTCTTTC[G/GTGCGTTGCCGAGCCGCAGCCGGTGATGACATCATTGC,A,C]
TGATTAGTCTCACACTTCTCACCATAATAAAAGATGCTATAACTGGTAATAATTTGATTAGCTCCTGGTTTGGAATGGTACATTCCTGGTTTGAAGATAG

Reverse complement sequence

CTATCTTCAAACCAGGAATGTACCATTCCAAACCAGGAGCTAATCAAATTATTACCAGTTATAGCATCTTTTATTATGGTGAGAAGTGTGAGACTAATCA[C/GCAATGATGTCATCACCGGCTGCGGCTCGGCAACGCAC,T,G]
GAAAGACATTGTTAGACCCACCCATAACCGCGGGCACGGCTATTCGAATAGTTTTACTCTAGCCAGAGGTGTACCACTGTGAAATGGATGTTTATAGTAA

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	74.60%	4.20%	8.95%	11.89%	GTGCGTTGCCGAGCCGCAGCCGGTGATGACATCATTGC: 0.23%; C: 0.15%
All Indica	2759	74.70%	0.20%	13.52%	10.91%	GTGCGTTGCCGAGCCGCAGCCGGTGATGACATCATTGC: 0.40%; C: 0.25%
All Japonica	1512	73.10%	12.00%	1.59%	13.36%	NA
Aus	269	78.80%	1.90%	5.58%	13.75%	NA
Indica I	595	71.60%	0.00%	20.17%	8.07%	GTGCGTTGCCGAGCCGCAGCCGGTGATGACATCATTGC: 0.17%
Indica II	465	62.60%	0.20%	20.22%	15.48%	C: 0.86%; GTGCGTTGCCGAGCCGCAGCCGGTGATGACATCATTGC: 0.65%
Indica III	913	83.40%	0.40%	5.37%	10.19%	GTGCGTTGCCGAGCCGCAGCCGGTGATGACATCATTGC: 0.55%; C: 0.11%
Indica Intermediate	786	74.20%	0.10%	13.99%	11.20%	C: 0.25%; GTGCGTTGCCGAGCCGCAGCCGGTGATGACATCATTGC: 0.25%
Temperate Japonica	767	97.10%	1.00%	0.26%	1.56%	NA
Tropical Japonica	504	36.30%	26.40%	3.37%	33.93%	NA
Japonica Intermediate	241	73.40%	16.60%	2.07%	7.88%	NA
VI/Aromatic	96	89.60%	0.00%	0.00%	10.42%	NA
Intermediate	90	68.90%	5.60%	12.22%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0818051811	G -> C	LOC_Os08g29440.1	downstream_gene_variant ; 1832.0bp to feature; MODIFIER	silent_mutation	Average:44.387; most accessible tissue: Minghui63 young leaf, score: 70.655	N	N	N	N
vg0818051811	G -> C	LOC_Os08g29450.1	downstream_gene_variant ; 2722.0bp to feature; MODIFIER	silent_mutation	Average:44.387; most accessible tissue: Minghui63 young leaf, score: 70.655	N	N	N	N
vg0818051811	G -> C	LOC_Os08g29440-LOC_Os08g29450	intergenic_region ; MODIFIER	silent_mutation	Average:44.387; most accessible tissue: Minghui63 young leaf, score: 70.655	N	N	N	N
vg0818051811	G -> A	LOC_Os08g29440.1	downstream_gene_variant ; 1832.0bp to feature; MODIFIER	silent_mutation	Average:44.387; most accessible tissue: Minghui63 young leaf, score: 70.655	N	N	N	N
vg0818051811	G -> A	LOC_Os08g29450.1	downstream_gene_variant ; 2722.0bp to feature; MODIFIER	silent_mutation	Average:44.387; most accessible tissue: Minghui63 young leaf, score: 70.655	N	N	N	N
vg0818051811	G -> A	LOC_Os08g29440-LOC_Os08g29450	intergenic_region ; MODIFIER	silent_mutation	Average:44.387; most accessible tissue: Minghui63 young leaf, score: 70.655	N	N	N	N
vg0818051811	G -> DEL	N	N	silent_mutation	Average:44.387; most accessible tissue: Minghui63 young leaf, score: 70.655	N	N	N	N
vg0818051811	G -> GTGCGTTGCCGAGCCGCAGCCGGTGATGAC ATCATTGC	LOC_Os08g29440.1	downstream_gene_variant ; 1833.0bp to feature; MODIFIER	silent_mutation	Average:44.387; most accessible tissue: Minghui63 young leaf, score: 70.655	N	N	N	N
vg0818051811	G -> GTGCGTTGCCGAGCCGCAGCCGGTGATGAC ATCATTGC	LOC_Os08g29450.1	downstream_gene_variant ; 2721.0bp to feature; MODIFIER	silent_mutation	Average:44.387; most accessible tissue: Minghui63 young leaf, score: 70.655	N	N	N	N
vg0818051811	G -> GTGCGTTGCCGAGCCGCAGCCGGTGATGAC ATCATTGC	LOC_Os08g29440-LOC_Os08g29450	intergenic_region ; MODIFIER	silent_mutation	Average:44.387; most accessible tissue: Minghui63 young leaf, score: 70.655	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818051811	NA	1.25E-06	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
vg0818051811	7.26E-07	2.64E-21	mr1301	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
vg0818051811	2.08E-08	3.70E-19	mr1410	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
vg0818051811	NA	6.15E-13	mr1410	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
vg0818051811	4.44E-07	NA	mr1533	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
vg0818051811	NA	1.50E-09	mr1533	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
vg0818051811	NA	1.31E-06	mr1836	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
vg0818051811	4.26E-06	NA	mr1980	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
vg0818051811	NA	3.45E-11	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
vg0818051811	NA	1.21E-06	mr1277_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
vg0818051811	7.12E-06	NA	mr1362_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
vg0818051811	NA	4.71E-07	mr1362_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
vg0818051811	4.44E-06	2.47E-16	mr1410_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
vg0818051811	NA	2.09E-12	mr1410_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
vg0818051811	NA	3.34E-11	mr1533_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
vg0818051811	NA	1.09E-07	mr1578_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
vg0818051811	NA	5.73E-09	mr1851_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