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Detailed information for vg0412042570:

Variant ID: vg0412042570 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12042570
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCGTTAGACCGTAGTCAATTTAACATCGGGGACACCCGCGCAACAAATATTGTATAAAAAACATGCTCTAGGTAAACATAATAAATTATTGATCTGACAA[C/T]
ATCTGAAAATAGGTACGGTAAATTGTGTATAAAATATTGCGTACCTTTATAGATACATGCCGGATGTATCTACGGGATTAGTAGATTAATTTAAAAAATC

Reverse complement sequence

GATTTTTTAAATTAATCTACTAATCCCGTAGATACATCCGGCATGTATCTATAAAGGTACGCAATATTTTATACACAATTTACCGTACCTATTTTCAGAT[G/A]
TTGTCAGATCAATAATTTATTATGTTTACCTAGAGCATGTTTTTTATACAATATTTGTTGCGCGGGTGTCCCCGATGTTAAATTGACTACGGTCTAACGC

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	67.60%	3.50%	7.07%	21.75%	NA
All Indica	2759	56.00%	5.90%	6.85%	31.24%	NA
All Japonica	1512	99.30%	0.10%	0.00%	0.66%	NA
Aus	269	2.20%	0.40%	49.07%	48.33%	NA
Indica I	595	77.10%	2.00%	2.52%	18.32%	NA
Indica II	465	51.60%	2.20%	6.02%	40.22%	NA
Indica III	913	49.20%	11.70%	9.53%	29.57%	NA
Indica Intermediate	786	50.40%	4.50%	7.51%	37.66%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	98.80%	0.00%	0.00%	1.19%	NA
Japonica Intermediate	241	98.30%	0.40%	0.00%	1.24%	NA
VI/Aromatic	96	86.50%	0.00%	6.25%	7.29%	NA
Intermediate	90	70.00%	1.10%	7.78%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412042570	C -> DEL	N	N	silent_mutation	Average:15.201; most accessible tissue: Callus, score: 81.847	N	N	N	N
vg0412042570	C -> T	LOC_Os04g21340.1	upstream_gene_variant ; 4450.0bp to feature; MODIFIER	silent_mutation	Average:15.201; most accessible tissue: Callus, score: 81.847	N	N	N	N
vg0412042570	C -> T	LOC_Os04g21330.1	intron_variant ; MODIFIER	silent_mutation	Average:15.201; most accessible tissue: Callus, score: 81.847	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412042570	2.40E-07	2.56E-07	mr1563	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
vg0412042570	NA	2.27E-07	mr1846	Ind_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
vg0412042570	NA	6.59E-08	mr1608_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
vg0412042570	NA	4.70E-10	mr1846_2	Ind_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