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Detailed information for vg0408384098:

Variant ID: vg0408384098 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 8384098
Reference Allele: C	Alternative Allele: T,A
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGCTTTTGGACCTGAGGATATCTTGTCTTGGAGTCAGCCAACGAAGTAAATTGGTCATTGGACTTTTTGAACATGGCCTTCTTCTTCACGCTCAACAAC[C/T,A]
AGGACTGTGCTTACAACCTGGGAAGTTGCTGACACGTATAACAACAGCGGCTCTTGCGGATGTGGCGAAGCTAGGTCTAGTGGAGTAGTGAGAAGTTTTT

Reverse complement sequence

AAAAACTTCTCACTACTCCACTAGACCTAGCTTCGCCACATCCGCAAGAGCCGCTGTTGTTATACGTGTCAGCAACTTCCCAGGTTGTAAGCACAGTCCT[G/A,T]
GTTGTTGAGCGTGAAGAAGAAGGCCATGTTCAAAAAGTCCAATGACCAATTTACTTCGTTGGCTGACTCCAAGACAAGATATCCTCAGGTCCAAAAGCTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.50%	0.60%	5.33%	16.38%	A: 0.17%
All Indica	2759	70.80%	0.60%	6.85%	21.78%	NA
All Japonica	1512	93.50%	0.60%	2.12%	3.31%	A: 0.53%
Aus	269	53.90%	0.40%	8.55%	37.17%	NA
Indica I	595	54.80%	0.00%	7.56%	37.65%	NA
Indica II	465	68.00%	0.00%	6.45%	25.59%	NA
Indica III	913	82.60%	1.40%	5.81%	10.19%	NA
Indica Intermediate	786	70.90%	0.40%	7.76%	20.99%	NA
Temperate Japonica	767	98.80%	0.00%	0.00%	1.17%	NA
Tropical Japonica	504	84.70%	1.60%	5.95%	6.35%	A: 1.39%
Japonica Intermediate	241	94.60%	0.40%	0.83%	3.73%	A: 0.41%
VI/Aromatic	96	82.30%	2.10%	1.04%	14.58%	NA
Intermediate	90	82.20%	0.00%	7.78%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0408384098	C -> DEL	LOC_Os04g14900.1	N	frameshift_variant	Average:6.84; most accessible tissue: Callus, score: 18.231	N	N	N	N
vg0408384098	C -> A	LOC_Os04g14900.1	missense_variant ; p.Trp61Leu; MODERATE	nonsynonymous_codon ; W61L	Average:6.84; most accessible tissue: Callus, score: 18.231	unknown	unknown	TOLERATED	0.16
vg0408384098	C -> T	LOC_Os04g14900.1	stop_gained ; p.Trp61*; HIGH	stop_gained	Average:6.84; most accessible tissue: Callus, score: 18.231	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0408384098	4.29E-07	5.32E-06	mr1748_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