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Detailed information for vg0405440340:

Variant ID: vg0405440340 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 5440340
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCTGCTGTAGCTGATGAATCCGAAGCCGATGAAGCAAAAAGATTGGCTCGGGGGAAGAGTGTTGTAACTGCATCGGTTAACATGGTTTTCACGTTACCT[G/T]
CTGAATTTGGAGCCAAACAAGCCGATGTCGATGAAGTTGAGGAAGCATCGGCTAGGTTGGTTTTGTCACCAGAGCAGGCGGTTTTTGAGAAACCATAGGG

Reverse complement sequence

CCCTATGGTTTCTCAAAAACCGCCTGCTCTGGTGACAAAACCAACCTAGCCGATGCTTCCTCAACTTCATCGACATCGGCTTGTTTGGCTCCAAATTCAG[C/A]
AGGTAACGTGAAAACCATGTTAACCGATGCAGTTACAACACTCTTCCCCCGAGCCAATCTTTTTGCTTCATCGGCTTCGGATTCATCAGCTACAGCAGCT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	45.20%	8.30%	5.01%	41.45%	NA
All Indica	2759	27.70%	1.10%	6.42%	64.73%	NA
All Japonica	1512	74.90%	22.70%	0.46%	1.98%	NA
Aus	269	62.80%	0.00%	8.92%	28.25%	NA
Indica I	595	26.40%	0.00%	6.39%	67.23%	NA
Indica II	465	29.20%	0.20%	6.88%	63.66%	NA
Indica III	913	22.60%	2.80%	6.35%	68.24%	NA
Indica Intermediate	786	33.80%	0.50%	6.23%	59.41%	NA
Temperate Japonica	767	73.50%	25.40%	0.65%	0.39%	NA
Tropical Japonica	504	71.20%	25.20%	0.40%	3.17%	NA
Japonica Intermediate	241	86.70%	8.70%	0.00%	4.56%	NA
VI/Aromatic	96	35.40%	8.30%	23.96%	32.29%	NA
Intermediate	90	40.00%	13.30%	6.67%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0405440340	G -> DEL	N	N	silent_mutation	Average:20.982; most accessible tissue: Zhenshan97 young leaf, score: 67.83	N	N	N	N
vg0405440340	G -> T	LOC_Os04g10080.1	downstream_gene_variant ; 3837.0bp to feature; MODIFIER	silent_mutation	Average:20.982; most accessible tissue: Zhenshan97 young leaf, score: 67.83	N	N	N	N
vg0405440340	G -> T	LOC_Os04g10070.1	intron_variant ; MODIFIER	silent_mutation	Average:20.982; most accessible tissue: Zhenshan97 young leaf, score: 67.83	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0405440340	2.67E-06	NA	mr1035	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
vg0405440340	NA	4.07E-06	mr1035	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
vg0405440340	4.54E-06	NA	mr1062	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
vg0405440340	NA	5.68E-09	mr1062	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
vg0405440340	NA	6.48E-07	mr1525	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
vg0405440340	1.47E-06	1.47E-06	mr1525	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
vg0405440340	1.91E-08	NA	mr1626	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
vg0405440340	6.13E-07	3.18E-08	mr1626	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
vg0405440340	8.71E-06	NA	mr1631	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
vg0405440340	4.67E-07	4.67E-07	mr1631	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
vg0405440340	5.15E-09	NA	mr1035_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
vg0405440340	1.14E-06	1.09E-08	mr1035_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
vg0405440340	1.95E-10	NA	mr1062_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
vg0405440340	8.10E-09	4.54E-11	mr1062_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
vg0405440340	3.44E-08	3.43E-08	mr1525_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
vg0405440340	1.82E-06	1.82E-06	mr1525_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
vg0405440340	2.62E-11	NA	mr1631_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
vg0405440340	6.88E-10	1.96E-13	mr1631_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