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Detailed information for vg1121138387:

Variant ID: vg1121138387 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21138387
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTCGTAGACACCCAACAGCGACGGCATAATAGGTCAGCTGTGTAGGCGGAGACACCAGTCGGCGGCGACGGAGGCAGGCTGGCGGTGAAGTCGTAGACG[T/C]
CCAACAACGGCGGCATAATAGGCCAGCCGTGTAGGCGGAGACACCAGTCGGCGGCGACGGAGGCAGGCCGGCGGTGAAGACGTAGACGCCCATGTACGGT

Reverse complement sequence

ACCGTACATGGGCGTCTACGTCTTCACCGCCGGCCTGCCTCCGTCGCCGCCGACTGGTGTCTCCGCCTACACGGCTGGCCTATTATGCCGCCGTTGTTGG[A/G]
CGTCTACGACTTCACCGCCAGCCTGCCTCCGTCGCCGCCGACTGGTGTCTCCGCCTACACAGCTGACCTATTATGCCGTCGCTGTTGGGTGTCTACGACT

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	89.20%	0.10%	7.83%	2.84%	NA
All Indica	2759	84.50%	0.00%	11.63%	3.84%	NA
All Japonica	1512	98.00%	0.00%	0.99%	0.99%	NA
Aus	269	84.40%	2.20%	9.67%	3.72%	NA
Indica I	595	97.10%	0.00%	1.51%	1.34%	NA
Indica II	465	82.80%	0.00%	14.62%	2.58%	NA
Indica III	913	78.30%	0.10%	15.77%	5.81%	NA
Indica Intermediate	786	83.10%	0.00%	12.72%	4.20%	NA
Temperate Japonica	767	97.30%	0.00%	0.78%	1.96%	NA
Tropical Japonica	504	98.60%	0.00%	1.39%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	90.00%	0.00%	6.67%	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
vg1121138387	T -> DEL	N	N	silent_mutation	Average:53.77; most accessible tissue: Zhenshan97 flag leaf, score: 75.761	N	N	N	N
vg1121138387	T -> C	LOC_Os11g35970.1	intron_variant ; MODIFIER	silent_mutation	Average:53.77; most accessible tissue: Zhenshan97 flag leaf, score: 75.761	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121138387	4.58E-06	4.58E-06	mr1469_2	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