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Detailed information for vg0122441656:

Variant ID: vg0122441656 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 22441656
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGTTAAAACAACGAGAGGCCCTTAATTATTATATCGGAGTAACATAATCTTCTTCTCCTTTTCTTCCCCTTCTTTTCGTTGGCCAAAACATCATTGAAT[T/C]
ATATACACACAAAAAGAACGCCCTCTTGTCCGTCAGCTAGCAATCTAAACAATCCACGTTCAAGTAAAGAGGATGAATCCGGGAGGTAAAAGAAAAAAAG

Reverse complement sequence

CTTTTTTTCTTTTACCTCCCGGATTCATCCTCTTTACTTGAACGTGGATTGTTTAGATTGCTAGCTGACGGACAAGAGGGCGTTCTTTTTGTGTGTATAT[A/G]
ATTCAATGATGTTTTGGCCAACGAAAAGAAGGGGAAGAAAAGGAGAAGAAGATTATGTTACTCCGATATAATAATTAAGGGCCTCTCGTTGTTTTAACTT

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	56.00%	0.20%	0.21%	43.57%	NA
All Indica	2759	40.40%	0.30%	0.36%	58.90%	NA
All Japonica	1512	94.80%	0.10%	0.00%	5.09%	NA
Aus	269	10.00%	0.70%	0.00%	89.22%	NA
Indica I	595	4.90%	0.50%	0.84%	93.78%	NA
Indica II	465	43.00%	0.60%	0.00%	56.34%	NA
Indica III	913	59.60%	0.10%	0.11%	40.20%	NA
Indica Intermediate	786	43.60%	0.10%	0.51%	55.73%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	86.50%	0.20%	0.00%	13.29%	NA
Japonica Intermediate	241	96.70%	0.00%	0.00%	3.32%	NA
VI/Aromatic	96	8.30%	0.00%	0.00%	91.67%	NA
Intermediate	90	67.80%	0.00%	0.00%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0122441656	T -> DEL	N	N	silent_mutation	Average:73.386; most accessible tissue: Zhenshan97 flag leaf, score: 85.514	N	N	N	N
vg0122441656	T -> C	LOC_Os01g39790.2	5_prime_UTR_premature_start_codon_gain_variant ; LOW	silent_mutation	Average:73.386; most accessible tissue: Zhenshan97 flag leaf, score: 85.514	N	N	N	N
vg0122441656	T -> C	LOC_Os01g39790.2	5_prime_UTR_variant ; 243.0bp to feature; MODIFIER	silent_mutation	Average:73.386; most accessible tissue: Zhenshan97 flag leaf, score: 85.514	N	N	N	N
vg0122441656	T -> C	LOC_Os01g39780.1	downstream_gene_variant ; 3264.0bp to feature; MODIFIER	silent_mutation	Average:73.386; most accessible tissue: Zhenshan97 flag leaf, score: 85.514	N	N	N	N
vg0122441656	T -> C	LOC_Os01g39800.1	downstream_gene_variant ; 4615.0bp to feature; MODIFIER	silent_mutation	Average:73.386; most accessible tissue: Zhenshan97 flag leaf, score: 85.514	N	N	N	N
vg0122441656	T -> C	LOC_Os01g39800.2	downstream_gene_variant ; 4554.0bp to feature; MODIFIER	silent_mutation	Average:73.386; most accessible tissue: Zhenshan97 flag leaf, score: 85.514	N	N	N	N
vg0122441656	T -> C	LOC_Os01g39790.1	intron_variant ; MODIFIER	silent_mutation	Average:73.386; most accessible tissue: Zhenshan97 flag leaf, score: 85.514	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0122441656	NA	4.03E-06	mr1095	Ind_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
vg0122441656	NA	2.38E-06	mr1123	Ind_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
vg0122441656	NA	1.15E-07	mr1245	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
vg0122441656	NA	2.03E-06	mr1380	Ind_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
vg0122441656	NA	5.58E-09	mr1439	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
vg0122441656	NA	9.69E-08	mr1561	Ind_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
vg0122441656	NA	2.57E-06	mr1835	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
vg0122441656	7.92E-07	NA	mr1875	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
vg0122441656	9.07E-08	9.07E-08	mr1875	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
vg0122441656	9.87E-08	NA	mr1908	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
vg0122441656	9.61E-07	2.85E-08	mr1908	Ind_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
vg0122441656	NA	3.71E-06	mr1936	Ind_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
vg0122441656	NA	7.68E-10	mr1124_2	Ind_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
vg0122441656	NA	1.02E-10	mr1222_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
vg0122441656	NA	2.06E-06	mr1380_2	Ind_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
vg0122441656	NA	7.15E-07	mr1561_2	Ind_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
vg0122441656	NA	1.28E-06	mr1908_2	Ind_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