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Detailed information for vg0121419136:

Variant ID: vg0121419136 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 21419136
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:

CTGTGTAGTCCTGCTCCACCATAGACGTTGTGCACCCTATCAACCCCCACGAACTGGTGCCACTACTGCCAATGCCGACCCGTGCACCACATGCCGCCGA[T/C]
GGTGCTCCCCACATCCTCCTCCCGCACCTCACTTGATCTACACCGTAACTGTCGTGGGCGTCGTCGCACGGTGTCCCCGCTCCGCTGCTGTCCTGACTGT

Reverse complement sequence

ACAGTCAGGACAGCAGCGGAGCGGGGACACCGTGCGACGACGCCCACGACAGTTACGGTGTAGATCAAGTGAGGTGCGGGAGGAGGATGTGGGGAGCACC[A/G]
TCGGCGGCATGTGGTGCACGGGTCGGCATTGGCAGTAGTGGCACCAGTTCGTGGGGGTTGATAGGGTGCACAACGTCTATGGTGGAGCAGGACTACACAG

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	36.30%	5.90%	1.59%	56.22%	NA
All Indica	2759	5.40%	3.00%	2.54%	89.05%	NA
All Japonica	1512	95.00%	0.30%	0.13%	4.56%	NA
Aus	269	4.10%	65.40%	1.12%	29.37%	NA
Indica I	595	3.90%	2.00%	1.68%	92.44%	NA
Indica II	465	9.00%	5.40%	2.80%	82.80%	NA
Indica III	913	2.30%	2.00%	2.52%	93.21%	NA
Indica Intermediate	786	7.90%	3.70%	3.05%	85.37%	NA
Temperate Japonica	767	96.00%	0.00%	0.13%	3.91%	NA
Tropical Japonica	504	95.20%	0.20%	0.00%	4.56%	NA
Japonica Intermediate	241	91.70%	1.20%	0.41%	6.64%	NA
VI/Aromatic	96	68.80%	12.50%	0.00%	18.75%	NA
Intermediate	90	58.90%	3.30%	0.00%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0121419136	T -> DEL	N	N	silent_mutation	Average:15.966; most accessible tissue: Callus, score: 46.094	N	N	N	N
vg0121419136	T -> C	LOC_Os01g38229.1	intron_variant ; MODIFIER	silent_mutation	Average:15.966; most accessible tissue: Callus, score: 46.094	N	N	N	N
vg0121419136	T -> C	LOC_Os01g38229.4	intron_variant ; MODIFIER	silent_mutation	Average:15.966; most accessible tissue: Callus, score: 46.094	N	N	N	N
vg0121419136	T -> C	LOC_Os01g38229.3	intron_variant ; MODIFIER	silent_mutation	Average:15.966; most accessible tissue: Callus, score: 46.094	N	N	N	N
vg0121419136	T -> C	LOC_Os01g38229.2	intron_variant ; MODIFIER	silent_mutation	Average:15.966; most accessible tissue: Callus, score: 46.094	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0121419136	NA	1.21E-28	mr1309	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
vg0121419136	1.03E-08	1.24E-08	mr1309	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
vg0121419136	NA	8.53E-08	mr1514	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
vg0121419136	NA	2.35E-23	mr1698	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
vg0121419136	3.57E-06	NA	mr1023_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
vg0121419136	NA	2.18E-27	mr1074_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
vg0121419136	NA	1.01E-14	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
vg0121419136	NA	3.86E-07	mr1205_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
vg0121419136	NA	5.15E-19	mr1239_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
vg0121419136	NA	4.51E-08	mr1681_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
vg0121419136	NA	2.19E-23	mr1698_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