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Detailed information for vg0413075261:

Variant ID: vg0413075261 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 13075261
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATTTCTGGGCGTGACACAAGTCCTCCGCCGTTACCACGAGAAGCGCATTCGAGCACGCATACTTTCGATCAGCGACTACGTCCTCCGACGGGTTCAAAG[C/T]
CAAGCAGGGCGAAACAAGCTCTCACCCAAATGGGAAGGACCTTACACGATCACACAAGTCTTGTGGCCAGGCGCATTCAAAATTGCAGACGGTGATGGTC

Reverse complement sequence

GACCATCACCGTCTGCAATTTTGAATGCGCCTGGCCACAAGACTTGTGTGATCGTGTAAGGTCCTTCCCATTTGGGTGAGAGCTTGTTTCGCCCTGCTTG[G/A]
CTTTGAACCCGTCGGAGGACGTAGTCGCTGATCGAAAGTATGCGTGCTCGAATGCGCTTCTCGTGGTAACGGCGGAGGACTTGTGTCACGCCCAGAAATT

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	79.80%	11.00%	3.17%	6.09%	NA
All Indica	2759	68.50%	18.60%	3.52%	9.39%	NA
All Japonica	1512	99.60%	0.10%	0.13%	0.20%	NA
Aus	269	74.70%	0.40%	17.47%	7.43%	NA
Indica I	595	91.90%	1.00%	1.34%	5.71%	NA
Indica II	465	79.40%	7.50%	9.25%	3.87%	NA
Indica III	913	46.10%	36.10%	2.52%	15.22%	NA
Indica Intermediate	786	70.40%	18.10%	2.93%	8.65%	NA
Temperate Japonica	767	99.70%	0.10%	0.00%	0.13%	NA
Tropical Japonica	504	99.40%	0.00%	0.20%	0.40%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	96.90%	0.00%	2.08%	1.04%	NA
Intermediate	90	87.80%	4.40%	2.22%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0413075261	C -> DEL	N	N	silent_mutation	Average:18.406; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0413075261	C -> T	LOC_Os04g23020.1	downstream_gene_variant ; 3475.0bp to feature; MODIFIER	silent_mutation	Average:18.406; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0413075261	C -> T	LOC_Os04g23030.1	downstream_gene_variant ; 284.0bp to feature; MODIFIER	silent_mutation	Average:18.406; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0413075261	C -> T	LOC_Os04g23020-LOC_Os04g23030	intergenic_region ; MODIFIER	silent_mutation	Average:18.406; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0413075261	2.25E-07	3.05E-10	mr1705_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