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Detailed information for vg0402260566:

Variant ID: vg0402260566 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2260566
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGCCACACGCATCAGCTTCAATAGTGAACTCCATAGAAAAGTCTGGCAAAGATAAAACTGGGCTGGTGCACATTTTCTATTTTAACTTATCAAAAGCTT[A/C]
TGTCTGTAAATTTCCCCACTGAAACAATTCTTTCTTCAGCATATCATGCAATGGCCTGCATATTAATCCATAGTTCTGAATGAATCTTCTATAATACCCA

Reverse complement sequence

TGGGTATTATAGAAGATTCATTCAGAACTATGGATTAATATGCAGGCCATTGCATGATATGCTGAAGAAAGAATTGTTTCAGTGGGGAAATTTACAGACA[T/G]
AAGCTTTTGATAAGTTAAAATAGAAAATGTGCACCAGCCCAGTTTTATCTTTGCCAGACTTTTCTATGGAGTTCACTATTGAAGCTGATGCGTGTGGCAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	26.50%	16.50%	1.04%	55.90%	NA
All Indica	2759	13.70%	11.80%	0.83%	73.65%	NA
All Japonica	1512	54.70%	14.20%	0.33%	30.82%	NA
Aus	269	3.70%	77.30%	1.49%	17.47%	NA
Indica I	595	5.70%	0.50%	1.18%	92.61%	NA
Indica II	465	3.70%	1.70%	0.65%	93.98%	NA
Indica III	913	20.80%	26.60%	0.66%	51.92%	NA
Indica Intermediate	786	17.60%	9.00%	0.89%	72.52%	NA
Temperate Japonica	767	87.70%	3.90%	0.13%	8.21%	NA
Tropical Japonica	504	18.50%	18.50%	0.79%	62.30%	NA
Japonica Intermediate	241	25.30%	37.80%	0.00%	36.93%	NA
VI/Aromatic	96	9.40%	18.80%	16.67%	55.21%	NA
Intermediate	90	31.10%	18.90%	1.11%	48.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402260566	A -> C	LOC_Os04g04710.1	stop_lost&splice_region_variant ; p.Ter731Gluext*?; HIGH	stop_lost	Average:10.268; most accessible tissue: Callus, score: 59.055	N	N	N	N
vg0402260566	A -> DEL	LOC_Os04g04710.1	N	frameshift_variant	Average:10.268; most accessible tissue: Callus, score: 59.055	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402260566	NA	1.98E-07	mr1798	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
vg0402260566	NA	4.93E-06	mr1404_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
vg0402260566	1.08E-06	5.66E-10	mr1798_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