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Detailed information for vg1001814606:

Variant ID: vg1001814606 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1814606
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCCGCTGCCCTCGGCAGAACTCACAAAGGGGGGCCTCACGGTTCCCCGGTGGAGGAGTTCATTCTCCGACATCTGGCGCGCCAGGTAGGGGGCGCGTTC[G/A]
TGATTTTTGAGGTTCTTTCGAGTGCCGGTGTGACGAGCGTCGCGGCGCCAAAGCGGGGGAAGGCGCAGCCTCCTCAGGAGTGTCGCGCCACCCCAGGCAG

Reverse complement sequence

CTGCCTGGGGTGGCGCGACACTCCTGAGGAGGCTGCGCCTTCCCCCGCTTTGGCGCCGCGACGCTCGTCACACCGGCACTCGAAAGAACCTCAAAAATCA[C/T]
GAACGCGCCCCCTACCTGGCGCGCCAGATGTCGGAGAATGAACTCCTCCACCGGGGAACCGTGAGGCCCCCCTTTGTGAGTTCTGCCGAGGGCAGCGGGT

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	76.50%	5.40%	16.23%	1.84%	NA
All Indica	2759	61.90%	9.20%	26.64%	2.17%	NA
All Japonica	1512	97.60%	0.00%	0.86%	1.59%	NA
Aus	269	97.00%	0.00%	2.60%	0.37%	NA
Indica I	595	56.30%	7.70%	33.61%	2.35%	NA
Indica II	465	51.40%	12.90%	32.26%	3.44%	NA
Indica III	913	71.60%	7.20%	19.93%	1.20%	NA
Indica Intermediate	786	61.20%	10.60%	25.83%	2.42%	NA
Temperate Japonica	767	99.30%	0.00%	0.65%	0.00%	NA
Tropical Japonica	504	94.40%	0.00%	0.79%	4.76%	NA
Japonica Intermediate	241	98.30%	0.00%	1.66%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	85.60%	0.00%	12.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1001814606	G -> A	LOC_Os10g03980.1	missense_variant ; p.Val46Met; MODERATE	nonsynonymous_codon ; V46M	Average:10.437; most accessible tissue: Zhenshan97 panicle, score: 16.188	unknown	unknown	TOLERATED	0.13
vg1001814606	G -> DEL	LOC_Os10g03980.1	N	frameshift_variant	Average:10.437; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001814606	3.84E-06	NA	mr1011_2	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