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Detailed information for vg0413844880:

Variant ID: vg0413844880 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 13844880
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATCTGACGTCCCTTAACTAATAAAAACCGGTCACAATAGATCCTTCGGTGGTTTTGACCCTGGTTTTTGTCTATGTGGCGACTGAGTCAGCGTGGGAC[C/T]
CACGTGTCAGGATGCCACGTCATCTCTCTTTCCCCTATTCTCTCCCTTCCTCAGATGGGGCCCACTTGTCAGGTGTCTCTTCTACCTCCTTCCCTGCGCC

Reverse complement sequence

GGCGCAGGGAAGGAGGTAGAAGAGACACCTGACAAGTGGGCCCCATCTGAGGAAGGGAGAGAATAGGGGAAAGAGAGATGACGTGGCATCCTGACACGTG[G/A]
GTCCCACGCTGACTCAGTCGCCACATAGACAAAAACCAGGGTCAAAACCACCGAAGGATCTATTGTGACCGGTTTTTATTAGTTAAGGGACGTCAGATAT

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	74.00%	7.10%	2.41%	16.50%	NA
All Indica	2759	64.30%	4.30%	3.88%	27.58%	NA
All Japonica	1512	90.70%	8.80%	0.20%	0.33%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	73.90%	12.10%	2.52%	11.43%	NA
Indica II	465	38.90%	0.90%	4.95%	55.27%	NA
Indica III	913	73.50%	0.70%	2.74%	23.11%	NA
Indica Intermediate	786	61.20%	4.60%	5.60%	28.63%	NA
Temperate Japonica	767	97.40%	2.30%	0.13%	0.13%	NA
Tropical Japonica	504	86.30%	13.30%	0.40%	0.00%	NA
Japonica Intermediate	241	78.40%	19.90%	0.00%	1.66%	NA
VI/Aromatic	96	26.00%	72.90%	0.00%	1.04%	NA
Intermediate	90	65.60%	15.60%	4.44%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0413844880	C -> DEL	N	N	silent_mutation	Average:62.354; most accessible tissue: Callus, score: 86.696	N	N	N	N
vg0413844880	C -> T	LOC_Os04g24200.1	upstream_gene_variant ; 1877.0bp to feature; MODIFIER	silent_mutation	Average:62.354; most accessible tissue: Callus, score: 86.696	N	N	N	N
vg0413844880	C -> T	LOC_Os04g24180.1	downstream_gene_variant ; 3619.0bp to feature; MODIFIER	silent_mutation	Average:62.354; most accessible tissue: Callus, score: 86.696	N	N	N	N
vg0413844880	C -> T	LOC_Os04g24180.2	downstream_gene_variant ; 3619.0bp to feature; MODIFIER	silent_mutation	Average:62.354; most accessible tissue: Callus, score: 86.696	N	N	N	N
vg0413844880	C -> T	LOC_Os04g24190.1	intron_variant ; MODIFIER	silent_mutation	Average:62.354; most accessible tissue: Callus, score: 86.696	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0413844880	1.77E-07	NA	mr1350_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0413844880	4.77E-07	3.87E-09	mr1350_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0413844880	3.30E-06	4.10E-07	mr1698_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
vg0413844880	4.66E-11	NA	mr1730_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0413844880	3.72E-06	3.81E-07	mr1730_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0413844880	2.40E-09	NA	mr1866_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251