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Detailed information for vg0412734026:

Variant ID: vg0412734026 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12734026
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGCAAGCTCTCAACATATCTTCCAGGATTTGATTGACTCGCTCGGTCTGACCATCAGTTTGCGGGTGATAGGCCGTGCTAAAATTTAAATGGGTCCCCAA[T/C]
TCTTCCTGCAGCTTCTGCCAGAATTTTGAGGTGAACTGACTCCCTCGATCAGATACAATCTTTTTGGGTACTCCATGTAGACACATGATTCTCGAAAGGT

Reverse complement sequence

ACCTTTCGAGAATCATGTGTCTACATGGAGTACCCAAAAAGATTGTATCTGATCGAGGGAGTCAGTTCACCTCAAAATTCTGGCAGAAGCTGCAGGAAGA[A/G]
TTGGGGACCCATTTAAATTTTAGCACGGCCTATCACCCGCAAACTGATGGTCAGACCGAGCGAGTCAATCAAATCCTGGAAGATATGTTGAGAGCTTGCG

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	39.10%	1.20%	52.09%	7.55%	NA
All Indica	2759	8.50%	2.10%	77.53%	11.92%	NA
All Japonica	1512	97.80%	0.00%	1.92%	0.33%	NA
Aus	269	0.70%	0.00%	92.19%	7.06%	NA
Indica I	595	2.90%	5.70%	71.76%	19.66%	NA
Indica II	465	6.20%	1.50%	76.13%	16.13%	NA
Indica III	913	14.50%	0.10%	79.63%	5.81%	NA
Indica Intermediate	786	7.10%	1.90%	80.28%	10.69%	NA
Temperate Japonica	767	97.70%	0.00%	2.09%	0.26%	NA
Tropical Japonica	504	98.80%	0.00%	0.79%	0.40%	NA
Japonica Intermediate	241	95.90%	0.00%	3.73%	0.41%	NA
VI/Aromatic	96	88.50%	0.00%	11.46%	0.00%	NA
Intermediate	90	56.70%	0.00%	38.89%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412734026	T -> C	LOC_Os04g22490.1	synonymous_variant ; p.Glu880Glu; LOW	synonymous_codon	Average:13.264; most accessible tissue: Zhenshan97 root, score: 27.411	N	N	N	N
vg0412734026	T -> DEL	LOC_Os04g22490.1	N	frameshift_variant	Average:13.264; most accessible tissue: Zhenshan97 root, score: 27.411	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412734026	1.65E-06	8.99E-06	mr1360_2	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