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Detailed information for vg0905075837:

Variant ID: vg0905075837 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 5075837
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATCTAGTGTGTGTTGTAACGCCCCGATTTTCGTTCGGGTTTTAAAATCATTTAATAATGCATTTCAAGAAATTATATTAAAAGTTAAAGCAATTTATTC[G/A]
AGTGAATTAATGGGAGAATTAAAATTTTCCCTTAAAAATCATTGGCCGGGAATATTTTGCAATATTCTTTTGCCCTAAAATACTCTCTGAAATTTCCTGT

Reverse complement sequence

ACAGGAAATTTCAGAGAGTATTTTAGGGCAAAAGAATATTGCAAAATATTCCCGGCCAATGATTTTTAAGGGAAAATTTTAATTCTCCCATTAATTCACT[C/T]
GAATAAATTGCTTTAACTTTTAATATAATTTCTTGAAATGCATTATTAAATGATTTTAAAACCCGAACGAAAATCGGGGCGTTACAACACACACTAGATC

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	88.70%	8.10%	1.99%	1.29%	NA
All Indica	2759	91.90%	7.50%	0.62%	0.00%	NA
All Japonica	1512	91.50%	0.20%	4.30%	3.97%	NA
Aus	269	38.30%	61.00%	0.74%	0.00%	NA
Indica I	595	95.50%	4.40%	0.17%	0.00%	NA
Indica II	465	92.70%	7.30%	0.00%	0.00%	NA
Indica III	913	94.00%	5.90%	0.11%	0.00%	NA
Indica Intermediate	786	86.40%	11.70%	1.91%	0.00%	NA
Temperate Japonica	767	85.80%	0.00%	7.43%	6.78%	NA
Tropical Japonica	504	99.20%	0.40%	0.00%	0.40%	NA
Japonica Intermediate	241	93.80%	0.40%	3.32%	2.49%	NA
VI/Aromatic	96	84.40%	5.20%	10.42%	0.00%	NA
Intermediate	90	95.60%	3.30%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0905075837	G -> DEL	N	N	silent_mutation	Average:37.705; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0905075837	G -> A	LOC_Os09g09430.1	intron_variant ; MODIFIER	silent_mutation	Average:37.705; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0905075837	NA	1.61E-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
vg0905075837	7.82E-06	4.74E-08	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
vg0905075837	NA	6.58E-06	mr1306_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
vg0905075837	NA	5.22E-06	mr1381_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
vg0905075837	NA	3.22E-07	mr1597_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
vg0905075837	NA	8.35E-06	mr1704_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
vg0905075837	NA	3.85E-06	mr1743_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
vg0905075837	3.45E-06	NA	mr1783_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
vg0905075837	5.83E-06	NA	mr1804_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
vg0905075837	7.11E-06	NA	mr1844_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
vg0905075837	1.23E-07	NA	mr1874_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
vg0905075837	9.19E-06	9.18E-06	mr1953_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