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Detailed information for vg0119413705:

Variant ID: vg0119413705 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 19413705
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCTCGGAAAGGAGCTGTGACAGTACCCCTCGCACAACACAATCCACCACAGCGCACCGTTCCTGGATCATAATCACCCCCTTATAAACAAGGCATGTACT[T/C]
CCCAGCGACCCCCGTGGGCTTATCTCCGCCACTTCTCAGTCTGGTGCTCCGTAATGAACCATGCTATACAAAAGGTAAAGCCGTTGCCCACGCTGGCTTG

Reverse complement sequence

CAAGCCAGCGTGGGCAACGGCTTTACCTTTTGTATAGCATGGTTCATTACGGAGCACCAGACTGAGAAGTGGCGGAGATAAGCCCACGGGGGTCGCTGGG[A/G]
AGTACATGCCTTGTTTATAAGGGGGTGATTATGATCCAGGAACGGTGCGCTGTGGTGGATTGTGTTGTGCGAGGGGTACTGTCACAGCTCCTTTCCGAGG

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	61.90%	1.70%	24.44%	11.93%	NA
All Indica	2759	36.30%	2.90%	40.49%	20.30%	NA
All Japonica	1512	99.50%	0.00%	0.53%	0.00%	NA
Aus	269	93.30%	0.40%	6.32%	0.00%	NA
Indica I	595	12.30%	3.50%	56.13%	28.07%	NA
Indica II	465	64.30%	2.80%	27.96%	4.95%	NA
Indica III	913	33.60%	2.00%	38.99%	25.41%	NA
Indica Intermediate	786	41.10%	3.60%	37.79%	17.56%	NA
Temperate Japonica	767	99.00%	0.00%	1.04%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	82.20%	0.00%	13.33%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0119413705	T -> DEL	N	N	silent_mutation	Average:32.827; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg0119413705	T -> C	LOC_Os01g35070.1	downstream_gene_variant ; 2174.0bp to feature; MODIFIER	silent_mutation	Average:32.827; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg0119413705	T -> C	LOC_Os01g35050-LOC_Os01g35070	intergenic_region ; MODIFIER	silent_mutation	Average:32.827; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0119413705	NA	1.20E-12	mr1565	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
vg0119413705	NA	5.93E-06	mr1053_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
vg0119413705	NA	1.48E-07	mr1072_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
vg0119413705	NA	2.82E-07	mr1075_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
vg0119413705	NA	3.14E-08	mr1077_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
vg0119413705	NA	1.08E-06	mr1232_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
vg0119413705	NA	9.10E-06	mr1510_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
vg0119413705	NA	3.71E-07	mr1539_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
vg0119413705	NA	3.45E-09	mr1557_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
vg0119413705	NA	1.03E-11	mr1565_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
vg0119413705	NA	2.71E-39	mr1598_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
vg0119413705	NA	8.91E-11	mr1598_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
vg0119413705	NA	1.71E-06	mr1901_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
vg0119413705	NA	1.10E-06	mr1959_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