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Detailed information for vg0619257211:

Variant ID: vg0619257211 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19257211
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCCAACTCACCCTAGGCTAGCGGAGACCAACACCTCTGACGGCCTTCTAGTAACTTGCCCGTCAGAGGTGGATGTCACCTGTGACGGCCGGCCACCCGT[T/C]
AAAGGTGACTGGACTCACCAGTGACCACTGATCACTGACCATGCGTGAAGCCGTCAAAGATGATGGTTTGGGTCCGTGACAGGTGACCTTGGCCAGTGTA

Reverse complement sequence

TACACTGGCCAAGGTCACCTGTCACGGACCCAAACCATCATCTTTGACGGCTTCACGCATGGTCAGTGATCAGTGGTCACTGGTGAGTCCAGTCACCTTT[A/G]
ACGGGTGGCCGGCCGTCACAGGTGACATCCACCTCTGACGGGCAAGTTACTAGAAGGCCGTCAGAGGTGTTGGTCTCCGCTAGCCTAGGGTGAGTTGGGA

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	67.40%	26.10%	0.21%	6.22%	NA
All Indica	2759	96.60%	3.00%	0.07%	0.36%	NA
All Japonica	1512	6.60%	74.40%	0.46%	18.52%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	95.80%	2.70%	0.17%	1.34%	NA
Indica II	465	95.50%	4.30%	0.22%	0.00%	NA
Indica III	913	99.10%	0.90%	0.00%	0.00%	NA
Indica Intermediate	786	94.90%	4.80%	0.00%	0.25%	NA
Temperate Japonica	767	3.70%	67.70%	0.91%	27.77%	NA
Tropical Japonica	504	11.70%	84.90%	0.00%	3.37%	NA
Japonica Intermediate	241	5.40%	73.90%	0.00%	20.75%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	64.40%	31.10%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0619257211	T -> C	LOC_Os06g33080.1	downstream_gene_variant ; 935.0bp to feature; MODIFIER	silent_mutation	Average:56.08; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg0619257211	T -> C	LOC_Os06g33070.1	intron_variant ; MODIFIER	silent_mutation	Average:56.08; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg0619257211	T -> DEL	N	N	silent_mutation	Average:56.08; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619257211	2.56E-09	3.04E-76	mr1033	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
vg0619257211	1.03E-06	NA	mr1033	Jap_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
vg0619257211	NA	1.47E-76	mr1100	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
vg0619257211	NA	4.69E-36	mr1105	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
vg0619257211	NA	6.04E-91	mr1140	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
vg0619257211	9.16E-06	3.85E-40	mr1176	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
vg0619257211	NA	6.80E-26	mr1223	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
vg0619257211	NA	8.62E-89	mr1395	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
vg0619257211	NA	5.04E-27	mr1423	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
vg0619257211	NA	1.13E-17	mr1529	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
vg0619257211	9.83E-06	NA	mr1536	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
vg0619257211	NA	6.40E-29	mr1546	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
vg0619257211	NA	1.64E-65	mr1619	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
vg0619257211	NA	5.77E-06	mr1925	Jap_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
vg0619257211	4.21E-10	3.48E-104	mr1033_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
vg0619257211	4.38E-06	NA	mr1536_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