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Detailed information for vg1208280442:

Variant ID: vg1208280442 (JBrowse)	Variation Type: INDEL
Chromosome: chr12	Position: 8280442
Reference Allele: CAT	Alternative Allele: C,TAT
Primary Allele: CAT	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGAACTGTTACACCTGTATACAAGCACGCAACATTCATTCTCCTCATGGAAAAAAAAAACAAGCTGTACAAAACAGTCGCAAAGAAAGTACAAGGACAAA[CAT/C,TAT]
GCATTTCCTTCATTCATATCGAGAAATAAGAAATACAGTACATATAAAAGAGCCAATTCGGAGGGTATTGCACAAATGAAAAGGGATTTGTTATACAACA

Reverse complement sequence

TGTTGTATAACAAATCCCTTTTCATTTGTGCAATACCCTCCGAATTGGCTCTTTTATATGTACTGTATTTCTTATTTCTCGATATGAATGAAGGAAATGC[ATG/G,ATA]
TTTGTCCTTGTACTTTCTTTGCGACTGTTTTGTACAGCTTGTTTTTTTTTTCCATGAGGAGAATGAATGTTGCGTGCTTGTATACAGGTGTAACAGTTCA

Allele Frequencies:

Populations	Population Size	Frequency of CAT(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.00%	20.70%	0.28%	25.84%	TAT: 7.22%
All Indica	2759	51.00%	1.30%	0.36%	35.85%	TAT: 11.42%
All Japonica	1512	42.90%	53.00%	0.13%	3.17%	TAT: 0.73%
Aus	269	17.80%	27.90%	0.00%	50.56%	TAT: 3.72%
Indica I	595	38.80%	0.80%	0.17%	42.52%	TAT: 17.65%
Indica II	465	45.80%	0.90%	0.65%	46.02%	TAT: 6.67%
Indica III	913	60.10%	1.50%	0.11%	27.93%	TAT: 10.30%
Indica Intermediate	786	52.80%	1.80%	0.64%	33.97%	TAT: 10.81%
Temperate Japonica	767	66.80%	26.70%	0.26%	4.82%	TAT: 1.43%
Tropical Japonica	504	14.10%	84.70%	0.00%	1.19%	NA
Japonica Intermediate	241	27.40%	70.50%	0.00%	2.07%	NA
VI/Aromatic	96	22.90%	34.40%	1.04%	40.62%	TAT: 1.04%
Intermediate	90	52.20%	33.30%	0.00%	10.00%	TAT: 4.44%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208280442	CAT -> C	LOC_Os12g14510.1	upstream_gene_variant ; 2938.0bp to feature; MODIFIER	silent_mutation	Average:31.245; most accessible tissue: Callus, score: 75.211	N	N	N	N
vg1208280442	CAT -> C	LOC_Os12g14500.1	intron_variant ; MODIFIER	silent_mutation	Average:31.245; most accessible tissue: Callus, score: 75.211	N	N	N	N
vg1208280442	CAT -> DEL	N	N	silent_mutation	Average:31.245; most accessible tissue: Callus, score: 75.211	N	N	N	N
vg1208280442	CAT -> TAT	LOC_Os12g14510.1	upstream_gene_variant ; 2939.0bp to feature; MODIFIER	silent_mutation	Average:31.245; most accessible tissue: Callus, score: 75.211	N	N	N	N
vg1208280442	CAT -> TAT	LOC_Os12g14500.1	intron_variant ; MODIFIER	silent_mutation	Average:31.245; most accessible tissue: Callus, score: 75.211	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208280442	NA	3.52E-06	mr1558_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
vg1208280442	4.40E-06	4.40E-06	mr1738_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