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Detailed information for vg0106048931:

Variant ID: vg0106048931 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 6048931
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACATTGGGTTGAATTGAGGTGCTTCAAGATGATTGCCGCACATGGATAGAGTCCTGAGAAGGCAATTGTATCTATTAATTAGGATGTTTTATGTAACTT[C/T]
CTTAGAGATATGTTTGGGCAAAAGTCTGCCGTAAAGACTTATGTTATCTTAGAGTTTGTTAGAGATAGTGATCGTGTCCGGTATAGACATATCTTGTAAT

Reverse complement sequence

ATTACAAGATATGTCTATACCGGACACGATCACTATCTCTAACAAACTCTAAGATAACATAAGTCTTTACGGCAGACTTTTGCCCAAACATATCTCTAAG[G/A]
AAGTTACATAAAACATCCTAATTAATAGATACAATTGCCTTCTCAGGACTCTATCCATGTGCGGCAATCATCTTGAAGCACCTCAATTCAACCCAATGTC

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	78.10%	8.70%	1.57%	11.66%	NA
All Indica	2759	77.20%	1.00%	2.14%	19.64%	NA
All Japonica	1512	74.20%	24.70%	0.99%	0.13%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.70%	0.00%	1.01%	0.34%	NA
Indica II	465	84.70%	0.60%	0.65%	13.98%	NA
Indica III	913	55.00%	0.20%	2.30%	42.50%	NA
Indica Intermediate	786	82.30%	2.90%	3.69%	11.07%	NA
Temperate Japonica	767	97.30%	2.70%	0.00%	0.00%	NA
Tropical Japonica	504	51.80%	45.40%	2.58%	0.20%	NA
Japonica Intermediate	241	47.70%	51.00%	0.83%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	80.00%	12.20%	0.00%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0106048931	C -> T	LOC_Os01g11280-LOC_Os01g11300	intergenic_region ; MODIFIER	silent_mutation	Average:17.839; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0106048931	C -> DEL	N	N	silent_mutation	Average:17.839; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0106048931	1.62E-06	NA	mr1925	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
vg0106048931	NA	1.47E-06	mr1691_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