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Detailed information for vg0431857188:

Variant ID: vg0431857188 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 31857188
Reference Allele: G	Alternative Allele: A,GC
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.69, G: 0.32, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

AAGATCAAGTACTTGAGAACCTTCGACCATGTAACAACCTCAAAGAGCTATTCATCATTGAACATGGAGGATCTACTTGCCCATCATGGCTAGGTGCAGA[G/A,GC]
CTCTCTGTGAAATCCTTGGAGACTCTTCATCTTTCCAATGTAACATGGAAAAACTTACCGCCGATAGGGGAGGTGTGTTTGGTAAACGGACTTGGTGAAG

Reverse complement sequence

CTTCACCAAGTCCGTTTACCAAACACACCTCCCCTATCGGCGGTAAGTTTTTCCATGTTACATTGGAAAGATGAAGAGTCTCCAAGGATTTCACAGAGAG[C/T,GC]
TCTGCACCTAGCCATGATGGGCAAGTAGATCCTCCATGTTCAATGATGAATAGCTCTTTGAGGTTGTTACATGGTCGAAGGTTCTCAAGTACTTGATCTT

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	48.30%	19.40%	2.45%	29.77%	GC: 0.04%
All Indica	2759	50.60%	22.40%	3.08%	23.85%	GC: 0.07%
All Japonica	1512	53.20%	11.10%	0.33%	35.32%	NA
Aus	269	9.30%	29.70%	2.60%	58.36%	NA
Indica I	595	48.90%	10.80%	2.86%	37.48%	NA
Indica II	465	63.70%	24.30%	0.86%	11.18%	NA
Indica III	913	37.70%	31.20%	4.71%	26.29%	GC: 0.11%
Indica Intermediate	786	59.00%	20.00%	2.67%	18.19%	GC: 0.13%
Temperate Japonica	767	84.20%	5.90%	0.26%	9.65%	NA
Tropical Japonica	504	14.10%	21.40%	0.20%	64.29%	NA
Japonica Intermediate	241	36.50%	6.20%	0.83%	56.43%	NA
VI/Aromatic	96	17.70%	29.20%	14.58%	38.54%	NA
Intermediate	90	46.70%	24.40%	5.56%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0431857188	G -> A	LOC_Os04g53496.1	N	synonymous_codon	Average:36.062; most accessible tissue: Callus, score: 80.593	N	N	N	N
vg0431857188	G -> DEL	LOC_Os04g53496.1	N	frameshift_variant	Average:36.062; most accessible tissue: Callus, score: 80.593	N	N	N	N
vg0431857188	G -> GC	LOC_Os04g53496.1	frameshift_variant ; p.Leu921fs; HIGH	frameshift_variant	Average:36.062; most accessible tissue: Callus, score: 80.593	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0431857188	3.25E-06	3.25E-06	mr1542	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
vg0431857188	8.12E-11	8.12E-11	mr1855	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
vg0431857188	NA	5.07E-06	mr1962	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