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Detailed information for vg0400002670:

Variant ID: vg0400002670 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2670
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGAAATTGTGCTTGTGTTTATATTTTTCTTGCACAAAGTTGAGGCATTACTTATTGTCCAATGAATGCACTGTGATATGCAAAGCCGATGTGGTTAAAT[G/A]
TATGCTGGCGGCTCCAGTTTTGAAAGGAAGAATTGGAAAATGGATATATGCTTTGACAGAGTTTGATCTCGGGTATGAATCACCCAAGGCGATAAAGGGG

Reverse complement sequence

CCCCTTTATCGCCTTGGGTGATTCATACCCGAGATCAAACTCTGTCAAAGCATATATCCATTTTCCAATTCTTCCTTTCAAAACTGGAGCCGCCAGCATA[C/T]
ATTTAACCACATCGGCTTTGCATATCACAGTGCATTCATTGGACAATAAGTAATGCCTCAACTTTGTGCAAGAAAAATATAAACACAAGCACAATTTCTC

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	25.90%	17.00%	0.80%	56.35%	NA
All Indica	2759	12.00%	2.40%	1.16%	84.41%	NA
All Japonica	1512	37.60%	47.10%	0.13%	15.21%	NA
Aus	269	97.00%	1.50%	0.37%	1.12%	NA
Indica I	595	1.80%	4.00%	1.85%	92.27%	NA
Indica II	465	5.60%	1.70%	1.29%	91.40%	NA
Indica III	913	12.90%	1.20%	0.55%	85.32%	NA
Indica Intermediate	786	22.50%	2.90%	1.27%	73.28%	NA
Temperate Japonica	767	11.70%	71.70%	0.26%	16.30%	NA
Tropical Japonica	504	65.70%	16.30%	0.00%	18.06%	NA
Japonica Intermediate	241	61.00%	33.20%	0.00%	5.81%	NA
VI/Aromatic	96	30.20%	1.00%	0.00%	68.75%	NA
Intermediate	90	36.70%	21.10%	3.33%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0400002670	G -> DEL	N	N	silent_mutation	Average:8.037; most accessible tissue: Callus, score: 35.121	N	N	N	N
vg0400002670	G -> A	LOC_Os04g01008.1	downstream_gene_variant ; 2281.0bp to feature; MODIFIER	silent_mutation	Average:8.037; most accessible tissue: Callus, score: 35.121	N	N	N	N
vg0400002670	G -> A	LOC_Os04g01006.1	intron_variant ; MODIFIER	silent_mutation	Average:8.037; most accessible tissue: Callus, score: 35.121	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0400002670	NA	1.37E-17	Plant_height	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0400002670	NA	5.76E-06	mr1279	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
vg0400002670	NA	3.47E-09	mr1578	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
vg0400002670	NA	2.29E-10	mr1696	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
vg0400002670	NA	4.19E-08	mr1942	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
vg0400002670	NA	1.41E-07	mr1236_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
vg0400002670	NA	7.24E-07	mr1252_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
vg0400002670	NA	3.53E-06	mr1252_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
vg0400002670	NA	3.56E-06	mr1263_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
vg0400002670	NA	4.68E-07	mr1263_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
vg0400002670	NA	1.95E-07	mr1295_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
vg0400002670	NA	1.23E-06	mr1346_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
vg0400002670	NA	1.55E-07	mr1456_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
vg0400002670	NA	2.92E-06	mr1550_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
vg0400002670	NA	5.56E-08	mr1563_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
vg0400002670	NA	9.07E-06	mr1729_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
vg0400002670	NA	7.59E-07	mr1792_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
vg0400002670	3.76E-06	NA	mr1793_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