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Detailed information for vg1104978159:

Variant ID: vg1104978159 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 4978159
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACAACAAGTGGTGGCGACGTTCCAAAAAAGGGGAGGAAATTCTCCTCTGTAATCGGACATCGTCGAAAGGCACCTACCCCCTCGGTAAGTTCTCCTGTCA[T/C]
TTGATCACGTAGTCAGAATACTTCCACCCCACATCATATCGATTGTACTCCAAGCCTTGGACGCGTCTCCCCTGCCTCCACGACGGCAGCGGCTTGTGAC

Reverse complement sequence

GTCACAAGCCGCTGCCGTCGTGGAGGCAGGGGAGACGCGTCCAAGGCTTGGAGTACAATCGATATGATGTGGGGTGGAAGTATTCTGACTACGTGATCAA[A/G]
TGACAGGAGAACTTACCGAGGGGGTAGGTGCCTTTCGACGATGTCCGATTACAGAGGAGAATTTCCTCCCCTTTTTTGGAACGTCGCCACCACTTGTTGT

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	79.00%	3.70%	2.33%	14.94%	NA
All Indica	2759	97.80%	0.10%	1.16%	0.87%	NA
All Japonica	1512	39.00%	11.30%	4.96%	44.71%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	98.20%	0.20%	0.84%	0.84%	NA
Indica II	465	99.80%	0.00%	0.00%	0.22%	NA
Indica III	913	99.10%	0.00%	0.77%	0.11%	NA
Indica Intermediate	786	94.90%	0.40%	2.54%	2.16%	NA
Temperate Japonica	767	39.90%	17.50%	3.78%	38.85%	NA
Tropical Japonica	504	38.30%	1.80%	7.14%	52.78%	NA
Japonica Intermediate	241	37.80%	11.60%	4.15%	46.47%	NA
VI/Aromatic	96	96.90%	0.00%	1.04%	2.08%	NA
Intermediate	90	94.40%	0.00%	1.11%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1104978159	T -> DEL	N	N	silent_mutation	Average:63.928; most accessible tissue: Minghui63 flag leaf, score: 82.053	N	N	N	N
vg1104978159	T -> C	LOC_Os11g09280.1	upstream_gene_variant ; 3095.0bp to feature; MODIFIER	silent_mutation	Average:63.928; most accessible tissue: Minghui63 flag leaf, score: 82.053	N	N	N	N
vg1104978159	T -> C	LOC_Os11g09280.2	upstream_gene_variant ; 3095.0bp to feature; MODIFIER	silent_mutation	Average:63.928; most accessible tissue: Minghui63 flag leaf, score: 82.053	N	N	N	N
vg1104978159	T -> C	LOC_Os11g09300.1	downstream_gene_variant ; 4575.0bp to feature; MODIFIER	silent_mutation	Average:63.928; most accessible tissue: Minghui63 flag leaf, score: 82.053	N	N	N	N
vg1104978159	T -> C	LOC_Os11g09290.1	intron_variant ; MODIFIER	silent_mutation	Average:63.928; most accessible tissue: Minghui63 flag leaf, score: 82.053	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1104978159	1.45E-07	NA	mr1019_2	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