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Detailed information for vg0403738024:

Variant ID: vg0403738024 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3738024
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGGTGGCCACAACCGAATCGATGTCATGATCACATATGTCTTGTTGGGCGGCGCTCTCGTCCTAGAGACGAGGTCGCTGCTGAAATCACTTTGTTCTAC[T/C]
TGGGGGCTAGTGTTCCTCTGCGACACACGCTGGAGCTGGCTTCGACATGTAGCTCTCTGCAGCGGAAGATGGCATCGGCTTCGGTACACAGTTCTCTCTT

Reverse complement sequence

AAGAGAGAACTGTGTACCGAAGCCGATGCCATCTTCCGCTGCAGAGAGCTACATGTCGAAGCCAGCTCCAGCGTGTGTCGCAGAGGAACACTAGCCCCCA[A/G]
GTAGAACAAAGTGATTTCAGCAGCGACCTCGTCTCTAGGACGAGAGCGCCGCCCAACAAGACATATGTGATCATGACATCGATTCGGTTGTGGCCACCTT

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	79.10%	19.30%	1.65%	0.00%	NA
All Indica	2759	88.20%	10.40%	1.38%	0.00%	NA
All Japonica	1512	58.80%	39.00%	2.25%	0.00%	NA
Aus	269	94.10%	5.20%	0.74%	0.00%	NA
Indica I	595	99.20%	0.50%	0.34%	0.00%	NA
Indica II	465	85.80%	13.10%	1.08%	0.00%	NA
Indica III	913	82.50%	15.90%	1.64%	0.00%	NA
Indica Intermediate	786	88.00%	9.90%	2.04%	0.00%	NA
Temperate Japonica	767	74.60%	23.60%	1.83%	0.00%	NA
Tropical Japonica	504	36.70%	60.30%	2.98%	0.00%	NA
Japonica Intermediate	241	54.80%	43.20%	2.07%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	82.20%	13.30%	4.44%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403738024	T -> C	LOC_Os04g07010.1	synonymous_variant ; p.Leu150Leu; LOW	synonymous_codon	Average:18.364; 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
vg0403738024	2.20E-06	3.85E-07	mr1697	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