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Detailed information for vg0121835801:

Variant ID: vg0121835801 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 21835801
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATCTCTACTAGTTAAAAAATAAGATGCTTGCTTCGTCCGTCAAAAAAAATAGCGAAAAAATAAAATTAAAAAGTCTGACTCCTATGTCCGATTCCCTTT[C/T]
AGAAAAGAAAAAAAAGTCTGATTCTACATTGGTGAAAAAAATTGATGTGCCGAATTAAAGATCTGTTTGCAAAAACGAAACCTACATGTCGAGAGCATTC

Reverse complement sequence

GAATGCTCTCGACATGTAGGTTTCGTTTTTGCAAACAGATCTTTAATTCGGCACATCAATTTTTTTCACCAATGTAGAATCAGACTTTTTTTTCTTTTCT[G/A]
AAAGGGAATCGGACATAGGAGTCAGACTTTTTAATTTTATTTTTTCGCTATTTTTTTTGACGGACGAAGCAAGCATCTTATTTTTTAACTAGTAGAGATA

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	48.80%	26.50%	1.31%	23.42%	NA
All Indica	2759	18.10%	44.80%	1.99%	35.12%	NA
All Japonica	1512	99.60%	0.20%	0.00%	0.20%	NA
Aus	269	53.50%	0.00%	1.86%	44.61%	NA
Indica I	595	1.80%	84.40%	4.03%	9.75%	NA
Indica II	465	24.30%	62.60%	2.80%	10.32%	NA
Indica III	913	15.10%	16.90%	0.44%	67.58%	NA
Indica Intermediate	786	30.20%	36.80%	1.78%	31.30%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.40%	0.00%	0.40%	NA
Japonica Intermediate	241	99.20%	0.40%	0.00%	0.41%	NA
VI/Aromatic	96	90.60%	0.00%	1.04%	8.33%	NA
Intermediate	90	76.70%	14.40%	1.11%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0121835801	C -> T	LOC_Os01g38900.1	downstream_gene_variant ; 1825.0bp to feature; MODIFIER	silent_mutation	Average:27.168; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0121835801	C -> T	LOC_Os01g38890-LOC_Os01g38900	intergenic_region ; MODIFIER	silent_mutation	Average:27.168; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0121835801	C -> DEL	N	N	silent_mutation	Average:27.168; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0121835801	NA	1.32E-07	mr1029	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
vg0121835801	3.55E-06	5.49E-06	mr1029	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
vg0121835801	NA	1.91E-10	mr1047	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
vg0121835801	7.44E-06	8.72E-06	mr1047	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
vg0121835801	NA	9.81E-08	mr1189	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
vg0121835801	NA	1.74E-10	mr1325	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
vg0121835801	NA	7.62E-06	mr1471	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
vg0121835801	NA	7.62E-07	mr1625	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
vg0121835801	NA	3.86E-06	mr1782	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
vg0121835801	NA	9.85E-09	mr1796	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
vg0121835801	NA	1.81E-07	mr1990	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
vg0121835801	NA	8.92E-16	mr1148_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
vg0121835801	NA	3.90E-11	mr1781_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