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Detailed information for vg1215445580:

Variant ID: vg1215445580 (JBrowse)	Variation Type: INDEL
Chromosome: chr12	Position: 15445580
Reference Allele: G	Alternative Allele: A,T,GCAAA
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGTGAGGCGAGTGAGGGCGTCGTGGCCAAGGTGACCGAGATGACGATGCCAAAGAACGTCGGAGGTGGTGCTGGCGGCGAGGGTGGTGGCGGTCGGTGG[G/A,T,GCAAA]
GAAGGTAGTGCTTGGTGGAGTGGGTAGAGCGGACCGGAGCTATTGAACCTGGCGATCACGGTCCTGGTGTGAAAATCCTTCACAGAGAAGCCAAAAGGGT

Reverse complement sequence

ACCCTTTTGGCTTCTCTGTGAAGGATTTTCACACCAGGACCGTGATCGCCAGGTTCAATAGCTCCGGTCCGCTCTACCCACTCCACCAAGCACTACCTTC[C/T,A,TTTGC]
CCACCGACCGCCACCACCCTCGCCGCCAGCACCACCTCCGACGTTCTTTGGCATCGTCATCTCGGTCACCTTGGCCACGACGCCCTCACTCGCCTCACCG

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	58.40%	5.90%	2.54%	30.72%	T: 2.39%; GCAAA: 0.02%
All Indica	2759	63.30%	8.20%	2.65%	24.68%	T: 1.16%; GCAAA: 0.04%
All Japonica	1512	60.30%	0.20%	1.79%	35.78%	T: 1.92%
Aus	269	14.50%	7.80%	5.58%	65.43%	T: 6.69%
Indica I	595	91.90%	0.20%	0.67%	7.23%	NA
Indica II	465	72.50%	6.20%	4.95%	14.84%	T: 1.51%
Indica III	913	37.60%	14.70%	2.96%	42.72%	T: 1.97%; GCAAA: 0.11%
Indica Intermediate	786	66.00%	7.90%	2.42%	22.77%	T: 0.89%
Temperate Japonica	767	91.30%	0.00%	0.91%	7.30%	T: 0.52%
Tropical Japonica	504	16.10%	0.20%	2.98%	79.76%	T: 0.99%
Japonica Intermediate	241	54.40%	0.80%	2.07%	34.44%	T: 8.30%
VI/Aromatic	96	13.50%	29.20%	3.12%	27.08%	T: 27.08%
Intermediate	90	57.80%	0.00%	2.22%	31.11%	T: 8.89%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215445580	G -> A	LOC_Os12g26430.1	missense_variant ; p.Gly21Arg; MODERATE	nonsynonymous_codon ; G21T	Average:31.106; most accessible tissue: Zhenshan97 flag leaf, score: 72.757	unknown	unknown	DELETERIOUS	0.00
vg1215445580	G -> A	LOC_Os12g26430.1	missense_variant ; p.Gly21Arg; MODERATE	nonsynonymous_codon ; G21R	Average:31.106; most accessible tissue: Zhenshan97 flag leaf, score: 72.757	unknown	unknown	DELETERIOUS	0.00
vg1215445580	G -> DEL	LOC_Os12g26430.1	N	frameshift_variant	Average:31.106; most accessible tissue: Zhenshan97 flag leaf, score: 72.757	N	N	N	N
vg1215445580	G -> GCAAA	LOC_Os12g26430.1	frameshift_variant ; p.Gly21fs; HIGH	frameshift_variant	Average:31.106; most accessible tissue: Zhenshan97 flag leaf, score: 72.757	N	N	N	N
vg1215445580	G -> T	LOC_Os12g26430.1	stop_gained ; p.Gly21*; HIGH	stop_gained	Average:31.106; most accessible tissue: Zhenshan97 flag leaf, score: 72.757	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215445580	6.11E-10	1.92E-10	mr1350_2	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
vg1215445580	NA	3.31E-06	mr1865_2	Jap_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