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Detailed information for vg0402168068:

Variant ID: vg0402168068 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2168068
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATCCGGCTGAGTAAAGATATATTTTAAACTCTTATGATCGGTATACACCTCTATACGAGTACCGAAAAGATAATGACGCCAAATTTTCAACGCATGAAC[C/T]
ACTGCAGCTAACTCAAGATCATGAGTAGGGTAGTTCTTCTCATGCGGACGTATCTGACGAGATGCATAGGCAACCACCTTCCCATCTTGCATCAGAACAC

Reverse complement sequence

GTGTTCTGATGCAAGATGGGAAGGTGGTTGCCTATGCATCTCGTCAGATACGTCCGCATGAGAAGAACTACCCTACTCATGATCTTGAGTTAGCTGCAGT[G/A]
GTTCATGCGTTGAAAATTTGGCGTCATTATCTTTTCGGTACTCGTATAGAGGTGTATACCGATCATAAGAGTTTAAAATATATCTTTACTCAGCCGGATC

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	55.80%	0.10%	3.53%	40.56%	NA
All Indica	2759	52.70%	0.10%	4.68%	42.52%	NA
All Japonica	1512	54.50%	0.00%	1.19%	44.31%	NA
Aus	269	85.10%	0.70%	3.72%	10.41%	NA
Indica I	595	61.50%	0.00%	1.85%	36.64%	NA
Indica II	465	40.00%	0.00%	6.24%	53.76%	NA
Indica III	913	57.70%	0.20%	6.13%	35.93%	NA
Indica Intermediate	786	47.80%	0.00%	4.20%	47.96%	NA
Temperate Japonica	767	75.70%	0.00%	0.52%	23.73%	NA
Tropical Japonica	504	28.60%	0.00%	1.79%	69.64%	NA
Japonica Intermediate	241	41.10%	0.00%	2.07%	56.85%	NA
VI/Aromatic	96	77.10%	0.00%	5.21%	17.71%	NA
Intermediate	90	62.20%	0.00%	5.56%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402168068	C -> DEL	LOC_Os04g04530.1	N	frameshift_variant	Average:8.499; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N
vg0402168068	C -> T	LOC_Os04g04530.1	synonymous_variant ; p.Val315Val; LOW	synonymous_codon	Average:8.499; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402168068	1.94E-07	3.40E-08	mr1633_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
vg0402168068	1.25E-07	6.06E-07	mr1633_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