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Detailed information for vg0432123700:

Variant ID: vg0432123700 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32123700
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGCTTCGGCGAACAATTGGCGACATCTTCTTCTTCGCAAACTAACCATCTAGTACTAGTGGAAATCCGAAGAAGGAAGAAGGGAGTAAACCTTTTGCAA[A/T]
TAGCATTAGGGGAAGGAGAAAAAAAAGGAACTTTCGCAAATAGTTTTATTTATAAAATATGTCCTTAGGTTTTATCCACTTGGCTTATCCTACAGTCGAG

Reverse complement sequence

CTCGACTGTAGGATAAGCCAAGTGGATAAAACCTAAGGACATATTTTATAAATAAAACTATTTGCGAAAGTTCCTTTTTTTTCTCCTTCCCCTAATGCTA[T/A]
TTGCAAAAGGTTTACTCCCTTCTTCCTTCTTCGGATTTCCACTAGTACTAGATGGTTAGTTTGCGAAGAAGAAGATGTCGCCAATTGTTCGCCGAAGCTC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.30%	0.20%	3.91%	38.57%	NA
All Indica	2759	47.10%	0.00%	4.49%	48.35%	NA
All Japonica	1512	66.00%	0.70%	3.64%	29.70%	NA
Aus	269	95.50%	0.00%	0.37%	4.09%	NA
Indica I	595	37.30%	0.00%	2.18%	60.50%	NA
Indica II	465	31.40%	0.00%	8.17%	60.43%	NA
Indica III	913	61.00%	0.00%	5.26%	33.73%	NA
Indica Intermediate	786	47.70%	0.10%	3.18%	48.98%	NA
Temperate Japonica	767	68.40%	0.00%	1.04%	30.51%	NA
Tropical Japonica	504	58.10%	1.80%	7.94%	32.14%	NA
Japonica Intermediate	241	74.70%	0.40%	2.90%	21.99%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	64.40%	0.00%	5.56%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0432123700	A -> DEL	N	N	silent_mutation	Average:8.379; most accessible tissue: Callus, score: 23.04	N	N	N	N
vg0432123700	A -> T	LOC_Os04g53910.1	downstream_gene_variant ; 4404.0bp to feature; MODIFIER	silent_mutation	Average:8.379; most accessible tissue: Callus, score: 23.04	N	N	N	N
vg0432123700	A -> T	LOC_Os04g53900.1	intron_variant ; MODIFIER	silent_mutation	Average:8.379; most accessible tissue: Callus, score: 23.04	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432123700	2.74E-06	1.41E-06	mr1557	Jap_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