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Detailed information for vg0403290283:

Variant ID: vg0403290283 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3290283
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGCAAATTATCCACAATCTGAGATTTCTCGTCACTTTTTGAATGGTCTCGATATGTCTATTTGGGAGATGAAAGTTACATCTATTCAGGAGTCTGTGAA[C/T]
ATGTCTTCTTTGACTTTGGATTCGCTTTACACAAAACTGAAAACTCATGAGATGAATATTCTTTCTCGTAAAGGTGATTCTAAGTCTAGTGCTTTGGTTT

Reverse complement sequence

AAACCAAAGCACTAGACTTAGAATCACCTTTACGAGAAAGAATATTCATCTCATGAGTTTTCAGTTTTGTGTAAAGCGAATCCAAAGTCAAAGAAGACAT[G/A]
TTCACAGACTCCTGAATAGATGTAACTTTCATCTCCCAAATAGACATATCGAGACCATTCAAAAAGTGACGAGAAATCTCAGATTGTGGATAATTTGCAT

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	49.20%	0.10%	11.81%	38.83%	NA
All Indica	2759	43.30%	0.20%	15.98%	40.52%	NA
All Japonica	1512	58.60%	0.00%	4.23%	37.17%	NA
Aus	269	62.50%	0.40%	10.78%	26.39%	NA
Indica I	595	57.30%	0.20%	7.06%	35.46%	NA
Indica II	465	46.70%	0.00%	9.25%	44.09%	NA
Indica III	913	30.10%	0.00%	26.29%	43.59%	NA
Indica Intermediate	786	45.90%	0.60%	14.76%	38.68%	NA
Temperate Japonica	767	85.10%	0.00%	0.39%	14.47%	NA
Tropical Japonica	504	27.80%	0.00%	10.12%	62.10%	NA
Japonica Intermediate	241	38.60%	0.00%	4.15%	57.26%	NA
VI/Aromatic	96	31.20%	0.00%	15.62%	53.12%	NA
Intermediate	90	53.30%	0.00%	10.00%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403290283	C -> DEL	LOC_Os04g06290.1	N	frameshift_variant	Average:9.351; most accessible tissue: Callus, score: 16.341	N	N	N	N
vg0403290283	C -> T	LOC_Os04g06290.1	synonymous_variant ; p.Asn179Asn; LOW	synonymous_codon	Average:9.351; most accessible tissue: Callus, score: 16.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403290283	2.16E-06	NA	mr1362_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