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Detailed information for vg0922392672:

Variant ID: vg0922392672 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 22392672
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCTCCCCTGCTACTCAGCGTCGGCCTCCACGACGAGCGCATCGCCGACGTCGTCCACCGCCGTGCCGGCGCCGGCGACGGCGAGAGAAGGCTGAAGGTG[A/C]
AGCTTGGACGCCGCCGCGATAGCACGCTCGTCAAAGCGAGCGGAGGCGTTCTTTGAGCAGAGCACCACGGCGACGTCAATCGTAATTAACTGGAATGATA

Reverse complement sequence

TATCATTCCAGTTAATTACGATTGACGTCGCCGTGGTGCTCTGCTCAAAGAACGCCTCCGCTCGCTTTGACGAGCGTGCTATCGCGGCGGCGTCCAAGCT[T/G]
CACCTTCAGCCTTCTCTCGCCGTCGCCGGCGCCGGCACGGCGGTGGACGACGTCGGCGATGCGCTCGTCGTGGAGGCCGACGCTGAGTAGCAGGGGAGCC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.90%	15.10%	0.02%	0.00%	NA
All Indica	2759	76.40%	23.60%	0.04%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	79.90%	20.10%	0.00%	0.00%	NA
Indica I	595	83.70%	16.30%	0.00%	0.00%	NA
Indica II	465	90.50%	9.50%	0.00%	0.00%	NA
Indica III	913	63.40%	36.60%	0.00%	0.00%	NA
Indica Intermediate	786	77.60%	22.30%	0.13%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0922392672	A -> C	LOC_Os09g39000.1	missense_variant ; p.Lys455Gln; MODERATE	nonsynonymous_codon ; K455Q	Average:74.471; most accessible tissue: Zhenshan97 panicle, score: 86.432	unknown	unknown	TOLERATED	0.11

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0922392672	2.62E-06	NA	mr1865_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
vg0922392672	NA	9.99E-07	mr1865_2	Ind_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