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Detailed information for vg0729687346:

Variant ID: vg0729687346 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 29687346
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAAGTCTTTACGGCAGACTCTTGCCCAAACATATCTCTAAAGAAACTATTTAAAATATCATAATTAATAGATATAATTGCCTATCTGAGAGCCTATCTC[C/A]
ATCGTGACAATCCTTGTGTAGCACGTTAATCGATTCCAGAAACGGTTTCATAACCATCTCAATGAAATCGGCTGTATCGGCTTTATTGGCTGTTTTCTGT

Reverse complement sequence

ACAGAAAACAGCCAATAAAGCCGATACAGCCGATTTCATTGAGATGGTTATGAAACCGTTTCTGGAATCGATTAACGTGCTACACAAGGATTGTCACGAT[G/T]
GAGATAGGCTCTCAGATAGGCAATTATATCTATTAATTATGATATTTTAAATAGTTTCTTTAGAGATATGTTTGGGCAAGAGTCTGCCGTAAAGACTTAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.80%	21.40%	2.73%	26.05%	NA
All Indica	2759	76.40%	1.20%	3.88%	18.56%	NA
All Japonica	1512	2.00%	60.50%	0.53%	36.97%	NA
Aus	269	63.60%	11.20%	1.86%	23.42%	NA
Indica I	595	52.60%	0.50%	6.72%	40.17%	NA
Indica II	465	68.00%	1.90%	4.30%	25.81%	NA
Indica III	913	95.80%	0.10%	2.19%	1.86%	NA
Indica Intermediate	786	76.80%	2.40%	3.44%	17.30%	NA
Temperate Japonica	767	0.10%	93.10%	0.13%	6.65%	NA
Tropical Japonica	504	4.00%	14.50%	0.99%	80.56%	NA
Japonica Intermediate	241	3.70%	53.10%	0.83%	42.32%	NA
VI/Aromatic	96	11.50%	9.40%	0.00%	79.17%	NA
Intermediate	90	36.70%	30.00%	10.00%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0729687346	C -> DEL	N	N	silent_mutation	Average:14.734; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N
vg0729687346	C -> A	N	intergenic_region ; MODIFIER	silent_mutation	Average:14.734; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0729687346	NA	1.07E-10	mr1316	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
vg0729687346	1.66E-06	NA	mr1499	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
vg0729687346	NA	7.37E-12	mr1540	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
vg0729687346	NA	3.92E-11	mr1712	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
vg0729687346	NA	2.53E-08	mr1716	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
vg0729687346	NA	1.41E-08	mr1770	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
vg0729687346	NA	1.17E-09	mr1790	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
vg0729687346	NA	2.87E-24	mr1862	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
vg0729687346	NA	7.08E-07	mr1915	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
vg0729687346	NA	7.25E-09	mr1946	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
vg0729687346	NA	3.77E-06	mr1977	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
vg0729687346	NA	1.80E-06	mr1250_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
vg0729687346	NA	1.49E-07	mr1446_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