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Detailed information for vg1101663368:

Variant ID: vg1101663368 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 1663368
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATAGCACTCAATATCCTCAACAGCAGATAGGAAACGATGTTCAAGTAGAAAAATTAATTTCATGTTCCACTATTGTAAAAGAGAAAGACTACTGTTCAA[T/A]
GCAACCATGATGGAGCTTTTCATCTAAAAACCATGATGGAGCTTATGCAGAACACCAGAACAGCACATGGAACTTCACCCCTAAAAAATATGCACAATTA

Reverse complement sequence

TAATTGTGCATATTTTTTAGGGGTGAAGTTCCATGTGCTGTTCTGGTGTTCTGCATAAGCTCCATCATGGTTTTTAGATGAAAAGCTCCATCATGGTTGC[A/T]
TTGAACAGTAGTCTTTCTCTTTTACAATAGTGGAACATGAAATTAATTTTTCTACTTGAACATCGTTTCCTATCTGCTGTTGAGGATATTGAGTGCTATC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.80%	1.10%	3.77%	6.37%	NA
All Indica	2759	82.70%	1.60%	5.87%	9.79%	NA
All Japonica	1512	99.70%	0.00%	0.00%	0.33%	NA
Aus	269	85.50%	1.50%	4.83%	8.18%	NA
Indica I	595	88.40%	1.20%	6.22%	4.20%	NA
Indica II	465	79.10%	2.20%	7.10%	11.61%	NA
Indica III	913	79.60%	2.40%	4.49%	13.47%	NA
Indica Intermediate	786	84.20%	0.60%	6.49%	8.65%	NA
Temperate Japonica	767	99.60%	0.00%	0.00%	0.39%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	2.10%	1.04%	1.04%	NA
Intermediate	90	92.20%	2.20%	2.22%	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
vg1101663368	T -> A	LOC_Os11g04104.3	intron_variant ; MODIFIER	silent_mutation	Average:45.415; most accessible tissue: Minghui63 young leaf, score: 61.887	N	N	N	N
vg1101663368	T -> A	LOC_Os11g04104.1	intron_variant ; MODIFIER	silent_mutation	Average:45.415; most accessible tissue: Minghui63 young leaf, score: 61.887	N	N	N	N
vg1101663368	T -> A	LOC_Os11g04104.2	intron_variant ; MODIFIER	silent_mutation	Average:45.415; most accessible tissue: Minghui63 young leaf, score: 61.887	N	N	N	N
vg1101663368	T -> DEL	N	N	silent_mutation	Average:45.415; most accessible tissue: Minghui63 young leaf, score: 61.887	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1101663368	1.55E-06	1.55E-06	mr1655	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