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Detailed information for vg0910741585:

Variant ID: vg0910741585 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10741585
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCGGGTTCACAAACACGCGCACCATTTGCGAGAGGCCGTGAGTTCTCTCGACGCCGTCGCTGAGGAGAAGGCGAGAGACTCGGGTGAGCGTGTAGGTGG[C/A]
CTCGCCGTCGCCGTCATGGACGGTAAAGATGCCGGAGAGAGTGAGCACGCGCATGAGCCGCCGAAGGTGGGAGAGCTTCGTCGGGTGCAGCCCGACATGG

Reverse complement sequence

CCATGTCGGGCTGCACCCGACGAAGCTCTCCCACCTTCGGCGGCTCATGCGCGTGCTCACTCTCTCCGGCATCTTTACCGTCCATGACGGCGACGGCGAG[G/T]
CCACCTACACGCTCACCCGAGTCTCTCGCCTTCTCCTCAGCGACGGCGTCGAGAGAACTCACGGCCTCTCGCAAATGGTGCGCGTGTTTGTGAACCCGGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.70%	8.20%	1.16%	0.00%	NA
All Indica	2759	98.60%	1.40%	0.00%	0.00%	NA
All Japonica	1512	75.10%	21.40%	3.44%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	94.80%	5.20%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.20%	0.80%	0.00%	0.00%	NA
Temperate Japonica	767	89.80%	4.60%	5.61%	0.00%	NA
Tropical Japonica	504	50.80%	48.20%	0.99%	0.00%	NA
Japonica Intermediate	241	79.30%	19.10%	1.66%	0.00%	NA
VI/Aromatic	96	88.50%	11.50%	0.00%	0.00%	NA
Intermediate	90	83.30%	13.30%	3.33%	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
vg0910741585	C -> A	LOC_Os09g17560.1	missense_variant ; p.Ala97Ser; MODERATE	nonsynonymous_codon ; A97S	Average:74.299; most accessible tissue: Zhenshan97 young leaf, score: 86.055	unknown	unknown	TOLERATED	0.34

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910741585	2.40E-06	NA	mr1519_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