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Detailed information for vg0400897236:

Variant ID: vg0400897236 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 897236
Reference Allele: C	Alternative Allele: T,CAAT
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTTCGGTGGAACAAAAAATGAAATGAATTCTCTTAATAGGGGGTTTCCAAAATATGTGGGTTTTTTTTGTTGCAATGGAATATTTCAGTGCACTGCAA[C/T,CAAT]
ATTAGATCTATACATAGTGAAATATTGTGAGTACACTAGATCGGGGGGAACGCCCGATTGGCTCCACCCCCGTCGGGCTCCCGAGCCCTGTCATTCTCCT

Reverse complement sequence

AGGAGAATGACAGGGCTCGGGAGCCCGACGGGGGTGGAGCCAATCGGGCGTTCCCCCCGATCTAGTGTACTCACAATATTTCACTATGTATAGATCTAAT[G/A,ATTG]
TTGCAGTGCACTGAAATATTCCATTGCAACAAAAAAAACCCACATATTTTGGAAACCCCCTATTAAGAGAATTCATTTCATTTTTTGTTCCACCGAAAAA

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	76.20%	18.90%	0.32%	2.31%	CAAT: 2.33%
All Indica	2759	64.00%	29.60%	0.54%	1.85%	CAAT: 3.91%
All Japonica	1512	93.70%	2.60%	0.00%	3.64%	CAAT: 0.07%
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	77.80%	16.60%	0.00%	0.00%	CAAT: 5.55%
Indica II	465	44.50%	44.70%	1.29%	7.96%	CAAT: 1.51%
Indica III	913	71.30%	25.10%	0.22%	0.22%	CAAT: 3.18%
Indica Intermediate	786	56.70%	35.90%	0.89%	1.53%	CAAT: 4.96%
Temperate Japonica	767	98.80%	1.20%	0.00%	0.00%	NA
Tropical Japonica	504	84.30%	5.00%	0.00%	10.71%	NA
Japonica Intermediate	241	96.70%	2.50%	0.00%	0.41%	CAAT: 0.41%
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	72.20%	23.30%	0.00%	3.33%	CAAT: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0400897236	C -> CAAT	LOC_Os04g02460.1	upstream_gene_variant ; 2638.0bp to feature; MODIFIER	silent_mutation	Average:35.963; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0400897236	C -> CAAT	LOC_Os04g02470.1	downstream_gene_variant ; 1248.0bp to feature; MODIFIER	silent_mutation	Average:35.963; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0400897236	C -> CAAT	LOC_Os04g02480.1	downstream_gene_variant ; 1769.0bp to feature; MODIFIER	silent_mutation	Average:35.963; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0400897236	C -> CAAT	LOC_Os04g02490.1	downstream_gene_variant ; 2568.0bp to feature; MODIFIER	silent_mutation	Average:35.963; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0400897236	C -> CAAT	LOC_Os04g02470-LOC_Os04g02480	intergenic_region ; MODIFIER	silent_mutation	Average:35.963; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0400897236	C -> DEL	N	N	silent_mutation	Average:35.963; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0400897236	C -> T	LOC_Os04g02460.1	upstream_gene_variant ; 2637.0bp to feature; MODIFIER	silent_mutation	Average:35.963; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0400897236	C -> T	LOC_Os04g02470.1	downstream_gene_variant ; 1247.0bp to feature; MODIFIER	silent_mutation	Average:35.963; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0400897236	C -> T	LOC_Os04g02480.1	downstream_gene_variant ; 1770.0bp to feature; MODIFIER	silent_mutation	Average:35.963; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0400897236	C -> T	LOC_Os04g02490.1	downstream_gene_variant ; 2569.0bp to feature; MODIFIER	silent_mutation	Average:35.963; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0400897236	C -> T	LOC_Os04g02470-LOC_Os04g02480	intergenic_region ; MODIFIER	silent_mutation	Average:35.963; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0400897236	5.35E-06	NA	mr1744_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
vg0400897236	1.06E-08	1.06E-08	mr1744_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