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Detailed information for vg0317228312:

Variant ID: vg0317228312 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 17228312
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGGATTCAAGTAATGCAAGCTAATCCCGTAGAAGTTCAGAATTCCCCGGAAGAATCTTGAGGTTGGAAGGGAGAAACCACCATAGAAGAAATGAGCAAA[C/T]
ACCACGATCTCGTGTGTATCGGGGGTCGGGAATGCTTCACCAAATGCCGGTCACCACCCGATGATTTCCTTCGCCGGAAGAACGCCGTGCGCCACCATCT

Reverse complement sequence

AGATGGTGGCGCACGGCGTTCTTCCGGCGAAGGAAATCATCGGGTGGTGACCGGCATTTGGTGAAGCATTCCCGACCCCCGATACACACGAGATCGTGGT[G/A]
TTTGCTCATTTCTTCTATGGTGGTTTCTCCCTTCCAACCTCAAGATTCTTCCGGGGAATTCTGAACTTCTACGGGATTAGCTTGCATTACTTGAATCCAA

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	37.90%	2.10%	0.78%	59.23%	NA
All Indica	2759	9.10%	0.30%	1.16%	89.42%	NA
All Japonica	1512	96.10%	0.10%	0.26%	3.51%	NA
Aus	269	11.90%	1.10%	0.37%	86.62%	NA
Indica I	595	9.40%	0.00%	1.18%	89.41%	NA
Indica II	465	12.90%	0.00%	1.51%	85.59%	NA
Indica III	913	6.70%	0.50%	0.99%	91.79%	NA
Indica Intermediate	786	9.40%	0.50%	1.15%	88.93%	NA
Temperate Japonica	767	99.60%	0.00%	0.13%	0.26%	NA
Tropical Japonica	504	89.50%	0.00%	0.60%	9.92%	NA
Japonica Intermediate	241	98.80%	0.80%	0.00%	0.41%	NA
VI/Aromatic	96	12.50%	77.10%	0.00%	10.42%	NA
Intermediate	90	45.60%	14.40%	0.00%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0317228312	C -> T	LOC_Os03g30180.1	downstream_gene_variant ; 3445.0bp to feature; MODIFIER	silent_mutation	Average:31.877; most accessible tissue: Minghui63 flower, score: 61.151	N	N	N	N
vg0317228312	C -> T	LOC_Os03g30190.1	intron_variant ; MODIFIER	silent_mutation	Average:31.877; most accessible tissue: Minghui63 flower, score: 61.151	N	N	N	N
vg0317228312	C -> DEL	N	N	silent_mutation	Average:31.877; most accessible tissue: Minghui63 flower, score: 61.151	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0317228312	NA	8.67E-07	mr1057	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
vg0317228312	9.86E-07	NA	mr1538	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
vg0317228312	1.49E-06	9.78E-07	mr1538	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