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Detailed information for vg0402180766:

Variant ID: vg0402180766 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2180766
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATCATTCTCAATTCCCTCAGTCTCAAGGTAACTGCCACGGTCACTTCCCTGTGGTTGGCGAGGATGGTAACGATACTCAGTGTCGGCCAACTGATCACT[A/G]
TAGCGATCACGAAGCTCTCCTATGGTGATCCTTGCCACCTCCTGACATACATGGATGTAGTTTCTTCCTCCAGCTTCGAACATCACTGAGGGGATATCTT

Reverse complement sequence

AAGATATCCCCTCAGTGATGTTCGAAGCTGGAGGAAGAAACTACATCCATGTATGTCAGGAGGTGGCAAGGATCACCATAGGAGAGCTTCGTGATCGCTA[T/C]
AGTGATCAGTTGGCCGACACTGAGTATCGTTACCATCCTCGCCAACCACAGGGAAGTGACCGTGGCAGTTACCTTGAGACTGAGGGAATTGAGAATGATG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	26.30%	0.20%	29.24%	44.24%	NA
All Indica	2759	15.50%	0.10%	41.21%	43.20%	NA
All Japonica	1512	49.10%	0.10%	5.49%	45.37%	NA
Aus	269	14.10%	1.90%	37.17%	46.84%	NA
Indica I	595	40.30%	0.20%	15.63%	43.87%	NA
Indica II	465	15.10%	0.20%	40.86%	43.87%	NA
Indica III	913	0.90%	0.00%	58.60%	40.53%	NA
Indica Intermediate	786	13.90%	0.10%	40.59%	45.42%	NA
Temperate Japonica	767	75.90%	0.00%	1.17%	22.95%	NA
Tropical Japonica	504	15.50%	0.20%	12.10%	72.22%	NA
Japonica Intermediate	241	34.00%	0.00%	5.39%	60.58%	NA
VI/Aromatic	96	9.40%	0.00%	31.25%	59.38%	NA
Intermediate	90	31.10%	0.00%	35.56%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402180766	A -> DEL	LOC_Os04g04560.1	N	frameshift_variant	Average:14.458; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg0402180766	A -> G	LOC_Os04g04560.1	synonymous_variant ; p.Tyr90Tyr; LOW	synonymous_codon	Average:14.458; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402180766	NA	1.23E-12	mr1182	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
vg0402180766	NA	5.59E-10	mr1182	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
vg0402180766	NA	1.46E-10	mr1282	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
vg0402180766	NA	5.93E-08	mr1282	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
vg0402180766	NA	4.56E-06	mr1330	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
vg0402180766	NA	7.05E-14	mr1650	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
vg0402180766	2.25E-06	1.19E-09	mr1650	Jap_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
vg0402180766	NA	5.31E-10	mr1658	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
vg0402180766	NA	8.84E-08	mr1658	Jap_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
vg0402180766	NA	4.38E-07	mr1763	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
vg0402180766	NA	1.97E-06	mr1880	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
vg0402180766	NA	2.25E-06	mr1182_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
vg0402180766	NA	1.07E-07	mr1880_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