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Detailed information for vg0413048245:

Variant ID: vg0413048245 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 13048245
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAATTCCGGGCGTGACAGAGCGTAAGCAAGCTTTTCCATTTCAATGTACCTTGTCTGCGCTCCTTGCAGTGCTTCGGAGACGAAGTAGACCGATTTCTGT[C/A]
TGGACTCTGTTTTTTGGACGAGTGCAGCACTGACTGCCACCGGCGAAGCTGCCAAGTATAATAGCAGTTCGCTTCCTCGGGGTGGGCTTATCAGAACTGG

Reverse complement sequence

CCAGTTCTGATAAGCCCACCCCGAGGAAGCGAACTGCTATTATACTTGGCAGCTTCGCCGGTGGCAGTCAGTGCTGCACTCGTCCAAAAAACAGAGTCCA[G/T]
ACAGAAATCGGTCTACTTCGTCTCCGAAGCACTGCAAGGAGCGCAGACAAGGTACATTGAAATGGAAAAGCTTGCTTACGCTCTGTCACGCCCGGAATTT

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	60.20%	11.70%	2.22%	25.84%	NA
All Indica	2759	39.90%	19.70%	3.23%	37.11%	NA
All Japonica	1512	95.30%	0.10%	0.00%	4.56%	NA
Aus	269	53.90%	0.40%	4.46%	41.26%	NA
Indica I	595	50.40%	1.00%	0.67%	47.90%	NA
Indica II	465	50.80%	10.80%	13.33%	25.16%	NA
Indica III	913	19.40%	36.60%	0.88%	43.15%	NA
Indica Intermediate	786	49.50%	19.60%	1.91%	29.01%	NA
Temperate Japonica	767	97.40%	0.10%	0.00%	2.48%	NA
Tropical Japonica	504	98.40%	0.00%	0.00%	1.59%	NA
Japonica Intermediate	241	82.20%	0.40%	0.00%	17.43%	NA
VI/Aromatic	96	96.90%	0.00%	0.00%	3.12%	NA
Intermediate	90	73.30%	6.70%	4.44%	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
vg0413048245	C -> DEL	LOC_Os04g22990.1	N	frameshift_variant	Average:9.826; most accessible tissue: Callus, score: 30.815	N	N	N	N
vg0413048245	C -> A	LOC_Os04g22990.1	missense_variant ; p.Arg2019Ile; MODERATE	nonsynonymous_codon ; R2019V	Average:9.826; most accessible tissue: Callus, score: 30.815	unknown	unknown	TOLERATED	0.35
vg0413048245	C -> A	LOC_Os04g22990.1	missense_variant ; p.Arg2019Ile; MODERATE	nonsynonymous_codon ; R2019I	Average:9.826; most accessible tissue: Callus, score: 30.815	unknown	unknown	TOLERATED	0.18

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0413048245	8.37E-06	NA	mr1705_2	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
vg0413048245	7.15E-07	1.11E-09	mr1705_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