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Detailed information for vg0910355345:

Variant ID: vg0910355345 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10355345
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGCTACAAGCCTTGCTTTATATCTCACCACCTCGTTGTTTTCATTCCGTTTCCGGACAAAAACCCATTTGTATCTCACAGGAAAGATACCACGAGGAGTA[G/A]
GCATTACAGCCGAGAATACATCTCTTTTGTAAAGCGAGGCTAATTCTGCGTCAATTACGTCCTTCCATTTGTTCCAGTCAGAGCGCTTTTGGCACTCTTT

Reverse complement sequence

AAAGAGTGCCAAAAGCGCTCTGACTGGAACAAATGGAAGGACGTAATTGACGCAGAATTAGCCTCGCTTTACAAAAGAGATGTATTCTCGGCTGTAATGC[C/T]
TACTCCTCGTGGTATCTTTCCTGTGAGATACAAATGGGTTTTTGTCCGGAAACGGAATGAAAACAACGAGGTGGTGAGATATAAAGCAAGGCTTGTAGCA

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	40.60%	0.20%	11.62%	47.55%	NA
All Indica	2759	38.00%	0.00%	3.55%	58.39%	NA
All Japonica	1512	41.40%	0.70%	23.15%	34.79%	NA
Aus	269	59.10%	0.00%	18.96%	21.93%	NA
Indica I	595	13.80%	0.00%	3.70%	82.52%	NA
Indica II	465	55.90%	0.00%	3.23%	40.86%	NA
Indica III	913	44.50%	0.00%	3.07%	52.46%	NA
Indica Intermediate	786	38.30%	0.10%	4.20%	57.38%	NA
Temperate Japonica	767	64.50%	0.40%	10.04%	25.03%	NA
Tropical Japonica	504	9.90%	0.60%	40.08%	49.40%	NA
Japonica Intermediate	241	33.60%	1.70%	29.46%	35.27%	NA
VI/Aromatic	96	35.40%	0.00%	40.62%	23.96%	NA
Intermediate	90	56.70%	0.00%	12.22%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910355345	G -> DEL	LOC_Os09g16930.1	N	frameshift_variant	Average:6.635; most accessible tissue: Callus, score: 18.223	N	N	N	N
vg0910355345	G -> A	LOC_Os09g16930.1	missense_variant ; p.Pro587Leu; MODERATE	nonsynonymous_codon ; P587L	Average:6.635; most accessible tissue: Callus, score: 18.223	probably damaging	2.029	TOLERATED	0.38

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910355345	NA	9.29E-08	mr1680	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
vg0910355345	3.23E-06	NA	mr1933_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