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Detailed information for vg0308977626:

Variant ID: vg0308977626 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 8977626
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGAGTGCACGATTCCCGAGGCGCAACTGGGTGGTTACAAGGGAACATGATATATCAATTAACAAAGGAAGGATCAAATGCAACAAATTAGGTAGGTCCGC[T/C]
AATCTGCCTTGCAGACGGGACAACAGATTAAGTGCGACCCTATCAATGCATAATATTTTTCAAGCAACATAATTAAATTTCAAATATAGGCTCAAGATGT

Reverse complement sequence

ACATCTTGAGCCTATATTTGAAATTTAATTATGTTGCTTGAAAAATATTATGCATTGATAGGGTCGCACTTAATCTGTTGTCCCGTCTGCAAGGCAGATT[A/G]
GCGGACCTACCTAATTTGTTGCATTTGATCCTTCCTTTGTTAATTGATATATCATGTTCCCTTGTAACCACCCAGTTGCGCCTCGGGAATCGTGCACTCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.60%	3.20%	15.87%	22.30%	NA
All Indica	2759	43.10%	1.00%	22.15%	33.82%	NA
All Japonica	1512	91.10%	7.90%	0.33%	0.66%	NA
Aus	269	24.90%	0.70%	42.38%	31.97%	NA
Indica I	595	70.90%	0.00%	7.73%	21.34%	NA
Indica II	465	30.50%	1.50%	17.42%	50.54%	NA
Indica III	913	36.30%	1.20%	34.39%	28.15%	NA
Indica Intermediate	786	37.30%	1.10%	21.63%	39.95%	NA
Temperate Japonica	767	86.70%	12.30%	0.13%	0.91%	NA
Tropical Japonica	504	95.40%	3.80%	0.60%	0.20%	NA
Japonica Intermediate	241	95.90%	2.90%	0.41%	0.83%	NA
VI/Aromatic	96	83.30%	0.00%	10.42%	6.25%	NA
Intermediate	90	63.30%	4.40%	11.11%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0308977626	T -> C	LOC_Os03g16280.1	downstream_gene_variant ; 3055.0bp to feature; MODIFIER	silent_mutation	Average:18.891; most accessible tissue: Zhenshan97 flag leaf, score: 53.795	N	N	N	N
vg0308977626	T -> C	LOC_Os03g16280-LOC_Os03g16290	intergenic_region ; MODIFIER	silent_mutation	Average:18.891; most accessible tissue: Zhenshan97 flag leaf, score: 53.795	N	N	N	N
vg0308977626	T -> DEL	N	N	silent_mutation	Average:18.891; most accessible tissue: Zhenshan97 flag leaf, score: 53.795	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0308977626	3.42E-06	3.42E-06	mr1396	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