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Detailed information for vg0727091375:

Variant ID: vg0727091375 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 27091375
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCGACCTCTCACGGTGGCTCCCTCCTCGGAGGTTGAGCAACCGCGACGCCTTACGGTGGCTCCCTCCACGGAGGTTGAGCAACCGTACGTTCCCCTCTTC[C/G]
GCCGACGCTTGCCGAACGACACCGTCCCTGCGGCACGTGACGCCCGATCAGCTGGCACGCCCTTGGTCAGCGCCTCCTCGATCGGCGCTGCCCCGTCGGT

Reverse complement sequence

ACCGACGGGGCAGCGCCGATCGAGGAGGCGCTGACCAAGGGCGTGCCAGCTGATCGGGCGTCACGTGCCGCAGGGACGGTGTCGTTCGGCAAGCGTCGGC[G/C]
GAAGAGGGGAACGTACGGTTGCTCAACCTCCGTGGAGGGAGCCACCGTAAGGCGTCGCGGTTGCTCAACCTCCGAGGAGGGAGCCACCGTGAGAGGTCGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.70%	4.30%	0.00%	0.00%	NA
All Indica	2759	99.40%	0.60%	0.00%	0.00%	NA
All Japonica	1512	94.00%	6.00%	0.00%	0.00%	NA
Aus	269	65.10%	34.90%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	98.20%	1.80%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	86.70%	13.30%	0.00%	0.00%	NA
Japonica Intermediate	241	90.90%	9.10%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0727091375	C -> G	LOC_Os07g45410.1	missense_variant ; p.Arg1589Gly; MODERATE	nonsynonymous_codon ; R1589G	Average:58.614; most accessible tissue: Zhenshan97 panicle, score: 76.605	unknown	unknown	TOLERATED	0.32

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0727091375	2.17E-07	2.17E-07	mr1200	Jap_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
vg0727091375	NA	1.44E-06	mr1665	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