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Detailed information for vg0401901910:

Variant ID: vg0401901910 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1901910
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTCTCCACTCTGGCCGCCTTTGTGTCGTAGCAGCCTAGCTCCATCGCCTCCGTAGTCAGCCATCTTCGAGTTGCCGAGTGGCAACCGTGTTCCCATGTC[G/A]
GCCACATCTGCTTACACTGCCGATTGCCTGAACAATTTCGCGGTCGGCTGCCTCCACGCCACCGCGTGGTGAACATGTCCCCGGGCTAGCCGGCACCAAC

Reverse complement sequence

GTTGGTGCCGGCTAGCCCGGGGACATGTTCACCACGCGGTGGCGTGGAGGCAGCCGACCGCGAAATTGTTCAGGCAATCGGCAGTGTAAGCAGATGTGGC[C/T]
GACATGGGAACACGGTTGCCACTCGGCAACTCGAAGATGGCTGACTACGGAGGCGATGGAGCTAGGCTGCTACGACACAAAGGCGGCCAGAGTGGAGACC

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	92.80%	5.10%	0.59%	1.46%	NA
All Indica	2759	99.30%	0.20%	0.07%	0.36%	NA
All Japonica	1512	79.10%	15.30%	1.72%	3.90%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	99.80%	0.10%	0.00%	0.11%	NA
Indica Intermediate	786	98.20%	0.40%	0.25%	1.15%	NA
Temperate Japonica	767	86.80%	3.40%	2.09%	7.69%	NA
Tropical Japonica	504	67.10%	31.00%	1.98%	0.00%	NA
Japonica Intermediate	241	79.70%	20.30%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401901910	G -> DEL	N	N	silent_mutation	Average:70.593; most accessible tissue: Zhenshan97 young leaf, score: 90.456	N	N	N	N
vg0401901910	G -> A	LOC_Os04g04130.1	upstream_gene_variant ; 3529.0bp to feature; MODIFIER	silent_mutation	Average:70.593; most accessible tissue: Zhenshan97 young leaf, score: 90.456	N	N	N	N
vg0401901910	G -> A	LOC_Os04g04120.1	intron_variant ; MODIFIER	silent_mutation	Average:70.593; most accessible tissue: Zhenshan97 young leaf, score: 90.456	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401901910	1.67E-07	2.81E-18	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
vg0401901910	NA	5.62E-12	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
vg0401901910	NA	4.86E-07	mr1668	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
vg0401901910	7.88E-06	NA	mr1104_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
vg0401901910	8.53E-07	1.40E-17	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
vg0401901910	NA	6.20E-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
vg0401901910	8.20E-08	NA	mr1798_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
vg0401901910	1.83E-06	NA	mr1798_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