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Detailed information for vg0407629042:

Variant ID: vg0407629042 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 7629042
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:

TGATGAAGACGATAGCCGATGGCTCGATAGCTGAGCATCAGGCTACAGGCCCGGTTTACTTGCAAGGAGGCGTTTTCCCGAATTATCGAGCTTTGGTCAC[T/C]
GATGCTCAGCCAGCTGTGCAGGCAGCTCCATCTGTCGCACCCGCGACTCAACCAACAGCGCCAGCGTCAACGCCCTTACCTGCTACATAAGCCACGGCGC

Reverse complement sequence

GCGCCGTGGCTTATGTAGCAGGTAAGGGCGTTGACGCTGGCGCTGTTGGTTGAGTCGCGGGTGCGACAGATGGAGCTGCCTGCACAGCTGGCTGAGCATC[A/G]
GTGACCAAAGCTCGATAATTCGGGAAAACGCCTCCTTGCAAGTAAACCGGGCCTGTAGCCTGATGCTCAGCTATCGAGCCATCGGCTATCGTCTTCATCA

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	47.50%	39.40%	10.18%	3.00%	NA
All Indica	2759	70.20%	12.90%	14.75%	2.10%	NA
All Japonica	1512	0.90%	92.60%	1.85%	4.63%	NA
Aus	269	84.80%	1.50%	12.64%	1.12%	NA
Indica I	595	86.20%	2.20%	10.59%	1.01%	NA
Indica II	465	62.20%	16.60%	19.78%	1.51%	NA
Indica III	913	68.60%	15.00%	13.47%	2.96%	NA
Indica Intermediate	786	64.80%	16.50%	16.41%	2.29%	NA
Temperate Japonica	767	0.40%	94.70%	2.09%	2.87%	NA
Tropical Japonica	504	1.80%	92.90%	0.20%	5.16%	NA
Japonica Intermediate	241	0.80%	85.50%	4.56%	9.13%	NA
VI/Aromatic	96	29.20%	56.20%	8.33%	6.25%	NA
Intermediate	90	40.00%	50.00%	4.44%	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
vg0407629042	T -> C	LOC_Os04g13660.1	synonymous_variant ; p.Thr213Thr; LOW	synonymous_codon	Average:16.953; most accessible tissue: Callus, score: 48.605	N	N	N	N
vg0407629042	T -> DEL	LOC_Os04g13660.1	N	frameshift_variant	Average:16.953; most accessible tissue: Callus, score: 48.605	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0407629042	2.46E-06	NA	mr1053	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