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Detailed information for vg0211327135:

Variant ID: vg0211327135 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 11327135
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCGAGTTCCTCCAGATCTACACCACGATCATCGTAGCGGCAAGGGGCGATGACCGGGTCATGGCGAATTATTTCCCCATGGCCCTCAAGGGTCAGGCGCG[T/C]
GGCTGGTTGATGACCCAGCCCCCCGACTCCATCTACTCCTGGGAGGACCTGTGCCAGCAGTTCATCACGAACTTCCAGGGCACATATCCCCGCCCAGGAG

Reverse complement sequence

CTCCTGGGCGGGGATATGTGCCCTGGAAGTTCGTGATGAACTGCTGGCACAGGTCCTCCCAGGAGTAGATGGAGTCGGGGGGCTGGGTCATCAACCAGCC[A/G]
CGCGCCTGACCCTTGAGGGCCATGGGGAAATAATTCGCCATGACCCGGTCATCGCCCCTTGCCGCTACGATGATCGTGGTGTAGATCTGGAGGAACTCGG

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	49.50%	0.50%	22.56%	27.44%	NA
All Indica	2759	18.00%	0.50%	36.43%	45.02%	NA
All Japonica	1512	98.60%	0.10%	0.33%	0.99%	NA
Aus	269	79.20%	1.90%	15.24%	3.72%	NA
Indica I	595	16.80%	0.00%	21.85%	61.34%	NA
Indica II	465	8.20%	0.00%	42.15%	49.68%	NA
Indica III	913	25.30%	1.00%	43.15%	30.56%	NA
Indica Intermediate	786	16.30%	0.80%	36.26%	46.69%	NA
Temperate Japonica	767	99.20%	0.00%	0.00%	0.78%	NA
Tropical Japonica	504	97.40%	0.20%	0.79%	1.59%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	93.80%	0.00%	3.12%	3.12%	NA
Intermediate	90	55.60%	1.10%	13.33%	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
vg0211327135	T -> DEL	LOC_Os02g19390.1	N	frameshift_variant	Average:19.163; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0211327135	T -> C	LOC_Os02g19390.1	synonymous_variant ; p.Arg94Arg; LOW	synonymous_codon	Average:19.163; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0211327135	T -> C	LOC_Os02g19390.1	synonymous_variant ; p.Arg94Arg; LOW	nonsynonymous_codon ; R94H	Average:19.163; most accessible tissue: Zhenshan97 panicle, score: 28.447	probably damaging	2.48	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0211327135	1.59E-06	1.59E-06	mr1341_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