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Detailed information for vg0416719847:

Variant ID: vg0416719847 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 16719847
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

CTAGTCATCCTAGTTGATTCAATTGACGCAGTTTGTTACATATTTACATATAAATTTCTATAGGTATATCGTAGACCACCCTTCCCTGATATATGGTGAT[C/A]
TATAGTATCTTTTTTTTTTAAAAAAAAAAAGAAAATACCTAATCAATATGAGTCCGAACATATTAGTTTAATAATTACAAAAATAACTTCTCAACCAACT

Reverse complement sequence

AGTTGGTTGAGAAGTTATTTTTGTAATTATTAAACTAATATGTTCGGACTCATATTGATTAGGTATTTTCTTTTTTTTTTTAAAAAAAAAAGATACTATA[G/T]
ATCACCATATATCAGGGAAGGGTGGTCTACGATATACCTATAGAAATTTATATGTAAATATGTAACAAACTGCGTCAATTGAATCAACTAGGATGACTAG

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	95.30%	3.20%	1.46%	0.04%	NA
All Indica	2759	94.10%	4.30%	1.52%	0.07%	NA
All Japonica	1512	96.30%	2.10%	1.65%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	79.30%	16.60%	4.03%	0.00%	NA
Indica II	465	98.10%	0.60%	0.86%	0.43%	NA
Indica III	913	99.60%	0.00%	0.44%	0.00%	NA
Indica Intermediate	786	96.60%	2.20%	1.27%	0.00%	NA
Temperate Japonica	767	93.00%	3.90%	3.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	2.20%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0416719847	C -> DEL	N	N	silent_mutation	Average:47.948; most accessible tissue: Minghui63 young leaf, score: 65.161	N	N	N	N
vg0416719847	C -> A	LOC_Os04g28270-LOC_Os04g28280	intergenic_region ; MODIFIER	silent_mutation	Average:47.948; most accessible tissue: Minghui63 young leaf, score: 65.161	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0416719847	NA	8.07E-07	mr1028	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
vg0416719847	9.19E-06	9.18E-06	mr1369	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
vg0416719847	NA	4.47E-06	mr1453	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
vg0416719847	NA	3.33E-06	mr1652	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
vg0416719847	2.58E-06	NA	mr1342_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
vg0416719847	NA	4.77E-06	mr1458_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
vg0416719847	7.18E-06	NA	mr1524_2	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