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Detailed information for vg0420179621:

Variant ID: vg0420179621 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 20179621
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCTCCAAGCATCCATCTTCCACACCTTGGACTAATGCACCTGAAAATCACTCAATGAACTCATTAGTCCCTTAACTACATTTGTCATTAATCACCAAAA[C/T]
CCACTAGGGGGATTAATGCACTTTCAATCTCCCCCTTTTTGGTGATTGATGACAACATGGTTAAAGCTTACAAAAGATTGAAATAAATTTTGTTTTGAAT

Reverse complement sequence

ATTCAAAACAAAATTTATTTCAATCTTTTGTAAGCTTTAACCATGTTGTCATCAATCACCAAAAAGGGGGAGATTGAAAGTGCATTAATCCCCCTAGTGG[G/A]
TTTTGGTGATTAATGACAAATGTAGTTAAGGGACTAATGAGTTCATTGAGTGATTTTCAGGTGCATTAGTCCAAGGTGTGGAAGATGGATGCTTGGAGAC

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	34.70%	5.10%	33.90%	26.32%	NA
All Indica	2759	18.20%	0.30%	41.65%	39.91%	NA
All Japonica	1512	64.20%	15.00%	14.29%	6.55%	NA
Aus	269	24.20%	0.00%	65.43%	10.41%	NA
Indica I	595	19.70%	0.00%	41.34%	38.99%	NA
Indica II	465	25.60%	0.00%	28.39%	46.02%	NA
Indica III	913	11.70%	0.10%	49.95%	38.23%	NA
Indica Intermediate	786	20.20%	0.80%	40.08%	38.93%	NA
Temperate Japonica	767	72.40%	15.50%	9.39%	2.74%	NA
Tropical Japonica	504	59.10%	6.90%	23.02%	10.91%	NA
Japonica Intermediate	241	48.50%	30.30%	11.62%	9.54%	NA
VI/Aromatic	96	54.20%	0.00%	42.71%	3.12%	NA
Intermediate	90	57.80%	5.60%	22.22%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0420179621	C -> DEL	N	N	silent_mutation	Average:14.404; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg0420179621	C -> T	LOC_Os04g33390-LOC_Os04g33330	intergenic_region ; MODIFIER	silent_mutation	Average:14.404; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0420179621	1.91E-06	1.90E-06	mr1197_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
vg0420179621	NA	6.82E-06	mr1510_2	Jap_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