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Detailed information for vg1128136971:

Variant ID: vg1128136971 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 28136971
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATATAGTTTTACATATTTCACAAAATTTTTTGAATAACACGAACAGTCAAACATATGCTAAAAAGTCAACAGAAACGGAGAATCAGTAAATCCATACGC[C/A]
CACCACTACTCAATGCCCAACTTTTGGTTTTGCTACTATCAGGAGTTGACGTCCACTCAACTATCATCATAACTGTGTCGTTGCCCATAAGTTTTGTGTG

Reverse complement sequence

CACACAAAACTTATGGGCAACGACACAGTTATGATGATAGTTGAGTGGACGTCAACTCCTGATAGTAGCAAAACCAAAAGTTGGGCATTGAGTAGTGGTG[G/T]
GCGTATGGATTTACTGATTCTCCGTTTCTGTTGACTTTTTAGCATATGTTTGACTGTTCGTGTTATTCAAAAAATTTTGTGAAATATGTAAAACTATATG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.30%	1.90%	3.72%	10.07%	NA
All Indica	2759	77.40%	2.80%	5.07%	14.75%	NA
All Japonica	1512	95.40%	0.70%	1.06%	2.84%	NA
Aus	269	94.10%	0.70%	2.60%	2.60%	NA
Indica I	595	73.90%	1.20%	5.88%	18.99%	NA
Indica II	465	74.60%	0.60%	4.95%	19.78%	NA
Indica III	913	78.00%	4.40%	5.26%	12.38%	NA
Indica Intermediate	786	81.00%	3.30%	4.33%	11.32%	NA
Temperate Japonica	767	96.20%	1.20%	1.30%	1.30%	NA
Tropical Japonica	504	94.80%	0.20%	0.40%	4.56%	NA
Japonica Intermediate	241	94.20%	0.00%	1.66%	4.15%	NA
VI/Aromatic	96	75.00%	2.10%	8.33%	14.58%	NA
Intermediate	90	88.90%	0.00%	5.56%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1128136971	C -> A	LOC_Os11g46860-LOC_Os11g46870	intergenic_region ; MODIFIER	silent_mutation	Average:17.82; most accessible tissue: Zhenshan97 flag leaf, score: 57.42	N	N	N	N
vg1128136971	C -> DEL	N	N	silent_mutation	Average:17.82; most accessible tissue: Zhenshan97 flag leaf, score: 57.42	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1128136971	1.48E-06	NA	mr1768_2	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