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Detailed information for vg0316786220:

Variant ID: vg0316786220 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 16786220
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAATGCAACAAGCAAAATTCTCACTCTCAATTTAGGCCGTGTTTAGATTTCAACTTTTTTCTTCAAACTTTTAACTTTTTCGTCACATCAAATGTTTAGG[C/T]
ACATATATAGAACATCAAATGTGGACGAAAAAAAACCAATTGCACAGTCCGACTGTAAATTGCGAGACGAATCTTTTGAGCCTAATTATGCCATGATTTG

Reverse complement sequence

CAAATCATGGCATAATTAGGCTCAAAAGATTCGTCTCGCAATTTACAGTCGGACTGTGCAATTGGTTTTTTTTCGTCCACATTTGATGTTCTATATATGT[G/A]
CCTAAACATTTGATGTGACGAAAAAGTTAAAAGTTTGAAGAAAAAAGTTGAAATCTAAACACGGCCTAAATTGAGAGTGAGAATTTTGCTTGTTGCATTT

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	72.20%	4.00%	1.99%	21.86%	NA
All Indica	2759	60.30%	0.10%	2.68%	36.82%	NA
All Japonica	1512	86.80%	11.80%	1.19%	0.20%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	55.10%	0.00%	3.87%	41.01%	NA
Indica II	465	89.70%	0.00%	1.08%	9.25%	NA
Indica III	913	48.40%	0.20%	2.52%	48.85%	NA
Indica Intermediate	786	60.80%	0.30%	2.93%	36.01%	NA
Temperate Japonica	767	99.50%	0.30%	0.26%	0.00%	NA
Tropical Japonica	504	64.90%	32.50%	1.98%	0.60%	NA
Japonica Intermediate	241	92.10%	5.40%	2.49%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	78.90%	5.60%	2.22%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0316786220	C -> T	LOC_Os03g29460.1	upstream_gene_variant ; 958.0bp to feature; MODIFIER	silent_mutation	Average:81.444; most accessible tissue: Minghui63 flag leaf, score: 85.5	N	N	N	N
vg0316786220	C -> T	LOC_Os03g29440.1	downstream_gene_variant ; 4542.0bp to feature; MODIFIER	silent_mutation	Average:81.444; most accessible tissue: Minghui63 flag leaf, score: 85.5	N	N	N	N
vg0316786220	C -> T	LOC_Os03g29440-LOC_Os03g29460	intergenic_region ; MODIFIER	silent_mutation	Average:81.444; most accessible tissue: Minghui63 flag leaf, score: 85.5	N	N	N	N
vg0316786220	C -> DEL	N	N	silent_mutation	Average:81.444; most accessible tissue: Minghui63 flag leaf, score: 85.5	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0316786220	2.30E-06	1.70E-08	mr1422	Jap_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