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Detailed information for vg1121617620:

Variant ID: vg1121617620 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21617620
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.52, C: 0.48, others allele: 0.00, population size: 46. )

Flanking Sequence (100 bp) in Reference Genome:

TCTCGAGGGTGCCCTTGCTGGCCAAGATCATCGTATCCAATACTGGAAGATGAAGTTTGAAGTGGCGGAACTCGAGAGAACCATGCTGGCAGTGAAGAAA[G/C]
AGCAGGCTGTGGAAACGCTCCAAGGTCGCGAGGTGTGGTTTAACTCGTACTTGAAGAGTTGCTGCACATCTATGGCCAGGGTCTGTAGAGAACTTCGAGT

Reverse complement sequence

ACTCGAAGTTCTCTACAGACCCTGGCCATAGATGTGCAGCAACTCTTCAAGTACGAGTTAAACCACACCTCGCGACCTTGGAGCGTTTCCACAGCCTGCT[C/G]
TTTCTTCACTGCCAGCATGGTTCTCTCGAGTTCCGCCACTTCAAACTTCATCTTCCAGTATTGGATACGATGATCTTGGCCAGCAAGGGCACCCTCGAGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.30%	21.60%	6.05%	10.07%	NA
All Indica	2759	54.90%	33.90%	7.32%	3.88%	NA
All Japonica	1512	72.90%	3.20%	3.17%	20.70%	NA
Aus	269	85.50%	2.60%	9.29%	2.60%	NA
Indica I	595	65.40%	13.30%	14.29%	7.06%	NA
Indica II	465	37.00%	54.60%	6.02%	2.37%	NA
Indica III	913	57.60%	36.00%	4.16%	2.19%	NA
Indica Intermediate	786	54.50%	34.70%	6.49%	4.33%	NA
Temperate Japonica	767	82.70%	1.30%	3.65%	12.39%	NA
Tropical Japonica	504	60.10%	6.30%	3.37%	30.16%	NA
Japonica Intermediate	241	68.90%	2.50%	1.24%	27.39%	NA
VI/Aromatic	96	44.80%	17.70%	7.29%	30.21%	NA
Intermediate	90	58.90%	14.40%	4.44%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121617620	G -> DEL	LOC_Os11g36630.1	N	frameshift_variant	Average:12.475; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N
vg1121617620	G -> C	LOC_Os11g36630.1	missense_variant ; p.Glu590Gln; MODERATE	nonsynonymous_codon ; E590Q	Average:12.475; most accessible tissue: Minghui63 root, score: 25.504	benign	1.135	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121617620	1.20E-06	7.78E-11	mr1053	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
vg1121617620	1.70E-08	8.52E-09	mr1053	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
vg1121617620	4.61E-07	1.54E-06	mr1070	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
vg1121617620	9.36E-06	NA	mr1128	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
vg1121617620	5.77E-08	4.27E-08	mr1128	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
vg1121617620	6.59E-06	7.04E-06	mr1139	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
vg1121617620	9.39E-06	1.16E-06	mr1145	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
vg1121617620	6.88E-08	9.66E-08	mr1147	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
vg1121617620	NA	3.44E-06	mr1283	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
vg1121617620	4.67E-06	2.12E-06	mr1436	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
vg1121617620	NA	7.27E-07	mr1709	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
vg1121617620	NA	7.74E-07	mr1709	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
vg1121617620	5.31E-06	NA	mr1913	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
vg1121617620	NA	1.68E-07	mr1913	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
vg1121617620	NA	1.36E-06	mr1956	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
vg1121617620	NA	5.57E-07	mr1027_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
vg1121617620	NA	5.50E-06	mr1053_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