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Detailed information for vg0429002025:

Variant ID: vg0429002025 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 29002025
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCCGATAGTTGACAAATACTTCAAGATACAGTTGATGAAGCAGTTCATCGCGCATTGTTTGAGTTTTGGCGAATACATTACAAAATTTGATCAAGGTAA[T/C]
AGTTGATGAGTTAATTATTTAGAAAAGCCAGCTCGGGGGGCAGATTGAAGAACAACAACAACATCGGCTCGGGGGGCAAGCACATCAGCGGCCAGAAGAA

Reverse complement sequence

TTCTTCTGGCCGCTGATGTGCTTGCCCCCCGAGCCGATGTTGTTGTTGTTCTTCAATCTGCCCCCCGAGCTGGCTTTTCTAAATAATTAACTCATCAACT[A/G]
TTACCTTGATCAAATTTTGTAATGTATTCGCCAAAACTCAAACAATGCGCGATGAACTGCTTCATCAACTGTATCTTGAAGTATTTGTCAACTATCGGCT

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	63.80%	1.20%	11.13%	23.87%	NA
All Indica	2759	41.10%	2.00%	18.05%	38.85%	NA
All Japonica	1512	99.80%	0.00%	0.00%	0.20%	NA
Aus	269	77.00%	0.00%	6.69%	16.36%	NA
Indica I	595	49.60%	1.20%	14.45%	34.79%	NA
Indica II	465	32.90%	1.30%	13.12%	52.69%	NA
Indica III	913	40.90%	3.20%	23.11%	32.86%	NA
Indica Intermediate	786	39.70%	1.80%	17.81%	40.71%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	80.00%	0.00%	10.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0429002025	T -> C	LOC_Os04g48650.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:12.972; most accessible tissue: Callus, score: 47.727	N	N	N	N
vg0429002025	T -> DEL	N	N	silent_mutation	Average:12.972; most accessible tissue: Callus, score: 47.727	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0429002025	3.64E-06	4.01E-06	mr1097_2	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