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Detailed information for vg0401798437:

Variant ID: vg0401798437 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1798437
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

CGTCTGCCCGAGAAGATATCTGATTGGCTGCGACCACGGCAAGCGAAGAAGAAGTGCCCACGACCAAGGTCTCGAAGAGCGGAGAAAGCGAAGCTAAGAC[C/T]
AAAAAGATTTCCCTAGATCCTTCTGATCCCACTAAAACTGCTGTAATAGGCTCCGAGTTAGACTGTAAATAGGAAAGCGCGCTCATCACCTTTCTTCAAA

Reverse complement sequence

TTTGAAGAAAGGTGATGAGCGCGCTTTCCTATTTACAGTCTAACTCGGAGCCTATTACAGCAGTTTTAGTGGGATCAGAAGGATCTAGGGAAATCTTTTT[G/A]
GTCTTAGCTTCGCTTTCTCCGCTCTTCGAGACCTTGGTCGTGGGCACTTCTTCTTCGCTTGCCGTGGTCGCAGCCAATCAGATATCTTCTCGGGCAGACG

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	24.20%	4.50%	12.55%	58.76%	NA
All Indica	2759	14.60%	4.00%	17.43%	64.04%	NA
All Japonica	1512	45.00%	6.40%	2.31%	46.30%	NA
Aus	269	16.00%	0.70%	15.99%	67.29%	NA
Indica I	595	4.70%	1.50%	10.59%	83.19%	NA
Indica II	465	27.50%	1.50%	21.72%	49.25%	NA
Indica III	913	14.20%	7.70%	18.95%	59.15%	NA
Indica Intermediate	786	14.80%	2.90%	18.32%	63.99%	NA
Temperate Japonica	767	75.60%	0.00%	0.78%	23.60%	NA
Tropical Japonica	504	5.60%	17.70%	3.77%	73.02%	NA
Japonica Intermediate	241	29.90%	3.30%	4.15%	62.66%	NA
VI/Aromatic	96	1.00%	2.10%	17.71%	79.17%	NA
Intermediate	90	21.10%	1.10%	18.89%	58.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401798437	C -> DEL	N	N	silent_mutation	Average:14.519; most accessible tissue: Callus, score: 30.303	N	N	N	N
vg0401798437	C -> T	LOC_Os04g03930.1	upstream_gene_variant ; 3454.0bp to feature; MODIFIER	silent_mutation	Average:14.519; most accessible tissue: Callus, score: 30.303	N	N	N	N
vg0401798437	C -> T	LOC_Os04g03950.1	downstream_gene_variant ; 3558.0bp to feature; MODIFIER	silent_mutation	Average:14.519; most accessible tissue: Callus, score: 30.303	N	N	N	N
vg0401798437	C -> T	LOC_Os04g03940.1	intron_variant ; MODIFIER	silent_mutation	Average:14.519; most accessible tissue: Callus, score: 30.303	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401798437	1.32E-06	3.36E-07	mr1666_2	Jap_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