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Detailed information for vg1005174294:

Variant ID: vg1005174294 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5174294
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTTGTCCTCTACTCCTACGATTTTTCTTTTGCCTGGGAGAACCACATGGCGCTTCGACTCGTCAGGCCCTTTGCTCTTCTTTCCTTTGCTAGACATGTC[C/T]
TTCACGTAAAAGACTTGCGTTACATCATTGGCAAGGACAAAAGGTTCGTCCGAGTATCCAACCTTGTTAAGGTCAACCGTTGTCATTGCACTGTCATCAA

Reverse complement sequence

TTGATGACAGTGCAATGACAACGGTTGACCTTAACAAGGTTGGATACTCGGACGAACCTTTTGTCCTTGCCAATGATGTAACGCAAGTCTTTTACGTGAA[G/A]
GACATGTCTAGCAAAGGAAAGAAGAGCAAAGGGCCTGACGAGTCGAAGCGCCATGTGGTTCTCCCAGGCAAAAGAAAAATCGTAGGAGTAGAGGACAAGA

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	90.50%	5.80%	3.55%	0.15%	NA
All Indica	2759	85.40%	9.70%	4.93%	0.00%	NA
All Japonica	1512	97.40%	0.20%	1.92%	0.46%	NA
Aus	269	98.90%	0.00%	1.12%	0.00%	NA
Indica I	595	86.70%	5.50%	7.73%	0.00%	NA
Indica II	465	83.40%	10.50%	6.02%	0.00%	NA
Indica III	913	89.40%	9.10%	1.53%	0.00%	NA
Indica Intermediate	786	80.80%	13.10%	6.11%	0.00%	NA
Temperate Japonica	767	96.30%	0.30%	2.87%	0.52%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	95.90%	0.40%	2.49%	1.24%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	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
vg1005174294	C -> T	LOC_Os10g09570-LOC_Os10g09590	intergenic_region ; MODIFIER	silent_mutation	Average:38.759; most accessible tissue: Minghui63 flag leaf, score: 59.912	N	N	N	N
vg1005174294	C -> DEL	N	N	silent_mutation	Average:38.759; most accessible tissue: Minghui63 flag leaf, score: 59.912	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005174294	2.84E-06	1.47E-06	mr1136	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