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Detailed information for vg1128487344:

Variant ID: vg1128487344 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 28487344
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCAGTTCTGAAACTAAGGCTGCGTTCGTTCATTCAGGTGAGATTGGGTGAGAAAGCGCATCGTTTTCCGCGCACACGCTGCCCAAACTACTAAACGGTA[C/T]
ATTTTTTGCAAAAAAATTTTATAGGAAAGTTGCTTTAAAAAATCATATTAATCTATTTTTGAAATCTAAAATAGTTAATACTCATATTAATTTCGTTTTA

Reverse complement sequence

TAAAACGAAATTAATATGAGTATTAACTATTTTAGATTTCAAAAATAGATTAATATGATTTTTTAAAGCAACTTTCCTATAAAATTTTTTTGCAAAAAAT[G/A]
TACCGTTTAGTAGTTTGGGCAGCGTGTGCGCGGAAAACGATGCGCTTTCTCACCCAATCTCACCTGAATGAACGAACGCAGCCTTAGTTTCAGAACTGAA

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	63.00%	2.60%	1.04%	33.41%	NA
All Indica	2759	47.90%	0.70%	1.27%	50.20%	NA
All Japonica	1512	89.20%	6.50%	0.33%	3.90%	NA
Aus	269	54.60%	0.00%	2.97%	42.38%	NA
Indica I	595	67.20%	0.00%	1.68%	31.09%	NA
Indica II	465	34.80%	0.20%	1.29%	63.66%	NA
Indica III	913	41.30%	1.60%	1.10%	55.97%	NA
Indica Intermediate	786	48.60%	0.30%	1.15%	50.00%	NA
Temperate Japonica	767	94.40%	1.00%	0.65%	3.91%	NA
Tropical Japonica	504	80.60%	16.70%	0.00%	2.78%	NA
Japonica Intermediate	241	90.90%	2.90%	0.00%	6.22%	NA
VI/Aromatic	96	93.80%	0.00%	0.00%	6.25%	NA
Intermediate	90	77.80%	4.40%	1.11%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1128487344	C -> T	LOC_Os11g47360.1	upstream_gene_variant ; 3814.0bp to feature; MODIFIER	silent_mutation	Average:35.231; most accessible tissue: Zhenshan97 root, score: 56.557	N	N	N	N
vg1128487344	C -> T	LOC_Os11g47350.1	downstream_gene_variant ; 842.0bp to feature; MODIFIER	silent_mutation	Average:35.231; most accessible tissue: Zhenshan97 root, score: 56.557	N	N	N	N
vg1128487344	C -> T	LOC_Os11g47350-LOC_Os11g47360	intergenic_region ; MODIFIER	silent_mutation	Average:35.231; most accessible tissue: Zhenshan97 root, score: 56.557	N	N	N	N
vg1128487344	C -> DEL	N	N	silent_mutation	Average:35.231; most accessible tissue: Zhenshan97 root, score: 56.557	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1128487344	NA	2.66E-06	mr1083	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
vg1128487344	3.21E-06	3.21E-06	mr1173	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