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Detailed information for vg1207676050:

Variant ID: vg1207676050 (JBrowse)	Variation Type: INDEL
Chromosome: chr12	Position: 7676050
Reference Allele: G	Alternative Allele: T,A,GT,GTTT
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGACAATTAGGCTGCTTGCAATTATGCAGTTGTTCCTTCAAAGATTATTCTGCAATGTTGTTCTTTTGTGTCAGTTGTGAGTTGAAGTTTAACTTCAAG[G/T,A,GT,GTTT]
TTTTTTTTCTAGGAGGATTTAAGCTCTTTTTGAAATTTCCAGATAGATTAGATTGGAAAAGGTATAGAGTTAATTTTATCAATTGATTATAGTTCTTATT

Reverse complement sequence

AATAAGAACTATAATCAATTGATAAAATTAACTCTATACCTTTTCCAATCTAATCTATCTGGAAATTTCAAAAAGAGCTTAAATCCTCCTAGAAAAAAAA[C/A,T,AC,AAAC]
CTTGAAGTTAAACTTCAACTCACAACTGACACAAAAGAACAACATTGCAGAATAATCTTTGAAGGAACAACTGCATAATTGCAAGCAGCCTAATTGTCTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.00%	10.20%	1.21%	0.00%	A: 0.53%; GT: 0.08%; GTTT: 0.02%
All Indica	2759	87.70%	10.50%	1.16%	0.00%	A: 0.43%; GT: 0.14%; GTTT: 0.04%
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	40.90%	49.40%	6.32%	0.00%	A: 3.35%
Indica I	595	78.30%	18.30%	2.86%	0.00%	A: 0.50%
Indica II	465	92.90%	6.20%	0.43%	0.00%	A: 0.22%; GTTT: 0.22%
Indica III	913	92.90%	6.40%	0.33%	0.00%	A: 0.44%
Indica Intermediate	786	85.90%	11.80%	1.27%	0.00%	GT: 0.51%; A: 0.51%
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	45.80%	46.90%	5.21%	0.00%	A: 2.08%
Intermediate	90	85.60%	8.90%	3.33%	0.00%	A: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1207676050	G -> GT	LOC_Os12g13650.1	frameshift_variant ; p.Leu31fs; HIGH	frameshift_variant	Average:42.078; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N
vg1207676050	G -> A	LOC_Os12g13650.1	missense_variant ; p.Val28Ile; MODERATE	nonsynonymous_codon ; V28I	Average:42.078; most accessible tissue: Zhenshan97 panicle, score: 63.607	unknown	unknown	DELETERIOUS	0.00
vg1207676050	G -> GTTT	LOC_Os12g13650.1	inframe_insertion ; p.Phe30dup; MODERATE	inframe_variant	Average:42.078; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N
vg1207676050	G -> T	LOC_Os12g13650.1	missense_variant ; p.Val28Phe; MODERATE	nonsynonymous_codon ; V28F	Average:42.078; most accessible tissue: Zhenshan97 panicle, score: 63.607	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207676050	2.39E-06	2.84E-07	mr1177	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
vg1207676050	NA	4.65E-07	mr1126_2	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