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Detailed information for vg0901431167:

Variant ID: vg0901431167 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 1431167
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGAGCGAACGAACGTGAACGAGAATTGAACGTGAAAGAACAAACGAACGTGAACTAACGAGCGTGAACGAACGTCAACGAACGTTAACGTGAACGAACGT[A/G]
AACTAACGAACGTGAACGTGCACGATCGTGAACAATAGTGAACGAACGTGAACGTGAAATGCAATATAGGCAGGTGAATGAACGTGAACGAACAAACGTA

Reverse complement sequence

TACGTTTGTTCGTTCACGTTCATTCACCTGCCTATATTGCATTTCACGTTCACGTTCGTTCACTATTGTTCACGATCGTGCACGTTCACGTTCGTTAGTT[T/C]
ACGTTCGTTCACGTTAACGTTCGTTGACGTTCGTTCACGCTCGTTAGTTCACGTTCGTTTGTTCTTTCACGTTCAATTCTCGTTCACGTTCGTTCGCTCG

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	88.50%	1.50%	5.46%	4.49%	NA
All Indica	2759	97.30%	0.10%	2.46%	0.14%	NA
All Japonica	1512	73.10%	4.30%	10.38%	12.24%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	98.80%	0.00%	1.18%	0.00%	NA
Indica II	465	99.80%	0.00%	0.00%	0.22%	NA
Indica III	913	97.00%	0.00%	2.85%	0.11%	NA
Indica Intermediate	786	94.90%	0.40%	4.45%	0.25%	NA
Temperate Japonica	767	98.70%	0.00%	0.26%	1.04%	NA
Tropical Japonica	504	39.50%	12.70%	26.19%	21.63%	NA
Japonica Intermediate	241	61.80%	0.40%	9.54%	28.22%	NA
VI/Aromatic	96	52.10%	4.20%	27.08%	16.67%	NA
Intermediate	90	85.60%	0.00%	7.78%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0901431167	A -> G	LOC_Os09g03040.1	intron_variant ; MODIFIER	silent_mutation	Average:26.934; most accessible tissue: Minghui63 flag leaf, score: 38.136	N	N	N	N
vg0901431167	A -> DEL	N	N	silent_mutation	Average:26.934; most accessible tissue: Minghui63 flag leaf, score: 38.136	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0901431167	1.62E-06	1.62E-06	mr1300	Ind_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