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Detailed information for vg0400894219:

Variant ID: vg0400894219 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 894219
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAACTAGGATCTTACTTCCCCGCTTCCCAAAATTCAGTGTATTACGTACTTGGTCCCGTTCTTGCTGAGCAACATCCGACTGGAGACCATCCAGCGCCAG[C/A]
AAGAACCTTTTGTCTCTCAATTCCGCTTTTAGCTTATTTTCTAGGGCATCAAGATTTTGGTACTTATAGGATGGTCGCCCAATGGCTCCTTCGAGCATCT

Reverse complement sequence

AGATGCTCGAAGGAGCCATTGGGCGACCATCCTATAAGTACCAAAATCTTGATGCCCTAGAAAATAAGCTAAAAGCGGAATTGAGAGACAAAAGGTTCTT[G/T]
CTGGCGCTGGATGGTCTCCAGTCGGATGTTGCTCAGCAAGAACGGGACCAAGTACGTAATACACTGAATTTTGGGAAGCGGGGAAGTAAGATCCTAGTTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.60%	3.60%	0.87%	23.97%	NA
All Indica	2759	68.90%	6.00%	1.01%	24.03%	NA
All Japonica	1512	73.00%	0.10%	0.60%	26.32%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	33.30%	2.00%	0.50%	64.20%	NA
Indica II	465	78.70%	2.60%	0.43%	18.28%	NA
Indica III	913	80.10%	10.10%	1.10%	8.76%	NA
Indica Intermediate	786	77.20%	6.40%	1.65%	14.76%	NA
Temperate Japonica	767	67.00%	0.10%	0.13%	32.72%	NA
Tropical Japonica	504	81.90%	0.00%	0.99%	17.06%	NA
Japonica Intermediate	241	73.40%	0.00%	1.24%	25.31%	NA
VI/Aromatic	96	36.50%	0.00%	4.17%	59.38%	NA
Intermediate	90	83.30%	1.10%	0.00%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0400894219	C -> DEL	LOC_Os04g02460.1	N	frameshift_variant	Average:42.018; most accessible tissue: Callus, score: 73.807	N	N	N	N
vg0400894219	C -> A	LOC_Os04g02460.1	missense_variant ; p.Leu127Phe; MODERATE	nonsynonymous_codon ; L127F	Average:42.018; most accessible tissue: Callus, score: 73.807	unknown	unknown	TOLERATED	0.52

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0400894219	NA	2.45E-06	mr1518	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
vg0400894219	3.29E-06	1.46E-08	mr1676	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
vg0400894219	NA	1.57E-06	mr1973	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
vg0400894219	2.05E-06	1.86E-10	mr1676_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