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Detailed information for vg1103697850:

Variant ID: vg1103697850 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 3697850
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACACCCATGTGGTCGCAATGTTGTATGGTCGGATGTAATTCCGAAGGAATCGGTCCTTAAATGCGACCGCACAAGTATTCCACCCAGGAATGGCCTTGTG[T/C]
CGCGAGTTTCATTTTTAAAACTCATTTTCTTTCACAAGGCACCGACTCAGGCATCGGGTTTTCCAAAGCTTTTGTAAACCAAGTTTTACCCAAGAAGTTA

Reverse complement sequence

TAACTTCTTGGGTAAAACTTGGTTTACAAAAGCTTTGGAAAACCCGATGCCTGAGTCGGTGCCTTGTGAAAGAAAATGAGTTTTAAAAATGAAACTCGCG[A/G]
CACAAGGCCATTCCTGGGTGGAATACTTGTGCGGTCGCATTTAAGGACCGATTCCTTCGGAATTACATCCGACCATACAACATTGCGACCACATGGGTGT

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	97.60%	2.30%	0.15%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	93.30%	6.40%	0.33%	0.00%	NA
Aus	269	96.30%	3.00%	0.74%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	99.50%	0.40%	0.13%	0.00%	NA
Tropical Japonica	504	84.30%	15.10%	0.60%	0.00%	NA
Japonica Intermediate	241	92.10%	7.50%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1103697850	T -> C	LOC_Os11g07330-LOC_Os11g07340	intergenic_region ; MODIFIER	silent_mutation	Average:18.041; most accessible tissue: Minghui63 flag leaf, score: 26.902	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1103697850	3.34E-06	6.98E-07	mr1095	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
vg1103697850	1.10E-06	1.10E-06	mr1098	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
vg1103697850	NA	2.10E-06	mr1101	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
vg1103697850	1.85E-06	1.85E-06	mr1589	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