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Detailed information for vg1120296880:

Variant ID: vg1120296880 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 20296880
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCAAAAGTTTGTGAATGGATTTTTAAGATACCTTAAAAAAATAGAATCCTTAAATTATTATTAAAAATAACAGTATCCAAACTTTAGTTTTCCCTTAAT[C/A]
TATGAGACAAAATTTTTAAACAAACAATAAAAATCCTACATTTTAATAATATAAGTGATTGCGCATGCGCGGGCCAACTTACTAGTTAACATAAAAAGAG

Reverse complement sequence

CTCTTTTTATGTTAACTAGTAAGTTGGCCCGCGCATGCGCAATCACTTATATTATTAAAATGTAGGATTTTTATTGTTTGTTTAAAAATTTTGTCTCATA[G/T]
ATTAAGGGAAAACTAAAGTTTGGATACTGTTATTTTTAATAATAATTTAAGGATTCTATTTTTTTAAGGTATCTTAAAAATCCATTCACAAACTTTTGAG

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	47.20%	9.00%	0.32%	43.50%	NA
All Indica	2759	39.60%	4.60%	0.33%	55.45%	NA
All Japonica	1512	48.70%	19.00%	0.33%	32.01%	NA
Aus	269	94.40%	1.90%	0.00%	3.72%	NA
Indica I	595	31.10%	0.00%	0.50%	68.40%	NA
Indica II	465	57.20%	0.60%	0.22%	41.94%	NA
Indica III	913	34.40%	11.40%	0.22%	54.00%	NA
Indica Intermediate	786	41.70%	2.50%	0.38%	55.34%	NA
Temperate Japonica	767	69.80%	15.30%	0.13%	14.86%	NA
Tropical Japonica	504	24.60%	31.70%	0.60%	43.06%	NA
Japonica Intermediate	241	32.00%	4.10%	0.41%	63.49%	NA
VI/Aromatic	96	92.70%	1.00%	1.04%	5.21%	NA
Intermediate	90	66.70%	3.30%	0.00%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1120296880	C -> A	LOC_Os11g34660.1	intron_variant ; MODIFIER	silent_mutation	Average:44.518; most accessible tissue: Zhenshan97 flower, score: 85.646	N	N	N	N
vg1120296880	C -> DEL	N	N	silent_mutation	Average:44.518; most accessible tissue: Zhenshan97 flower, score: 85.646	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120296880	8.99E-06	NA	mr1671_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