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Detailed information for vg1121302509:

Variant ID: vg1121302509 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21302509
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTCATGACTGTCCAACCGGGCTAAATACGGAGTACCCTCCCCAGGAAATTAACTTAGGACTATATACACGTGCGGAGGAATACCCGTACTGAGCTGTCA[C/T]
CATCAGCGGCCCACCTCGCTTCCGCAGCATATAACCCCAAATAATGATATCCAGTAATCTAAACACCACGCTTAAATTACCAAATACTACTCTAATATCA

Reverse complement sequence

TGATATTAGAGTAGTATTTGGTAATTTAAGCGTGGTGTTTAGATTACTGGATATCATTATTTGGGGTTATATGCTGCGGAAGCGAGGTGGGCCGCTGATG[G/A]
TGACAGCTCAGTACGGGTATTCCTCCGCACGTGTATATAGTCCTAAGTTAATTTCCTGGGGAGGGTACTCCGTATTTAGCCCGGTTGGACAGTCATGACG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.50%	3.90%	0.21%	2.39%	NA
All Indica	2759	98.00%	0.90%	0.25%	0.76%	NA
All Japonica	1512	91.10%	7.70%	0.00%	1.19%	NA
Aus	269	59.10%	12.30%	1.12%	27.51%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	97.60%	0.20%	0.00%	2.15%	NA
Indica III	913	97.80%	0.70%	0.55%	0.99%	NA
Indica Intermediate	786	97.20%	2.40%	0.13%	0.25%	NA
Temperate Japonica	767	95.40%	2.50%	0.00%	2.09%	NA
Tropical Japonica	504	84.50%	15.10%	0.00%	0.40%	NA
Japonica Intermediate	241	91.30%	8.70%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121302509	C -> T	LOC_Os11g36200.1	downstream_gene_variant ; 777.0bp to feature; MODIFIER	silent_mutation	Average:54.209; most accessible tissue: Minghui63 flag leaf, score: 68.16	N	N	N	N
vg1121302509	C -> T	LOC_Os11g36200.2	downstream_gene_variant ; 777.0bp to feature; MODIFIER	silent_mutation	Average:54.209; most accessible tissue: Minghui63 flag leaf, score: 68.16	N	N	N	N
vg1121302509	C -> T	LOC_Os11g36200-LOC_Os11g36210	intergenic_region ; MODIFIER	silent_mutation	Average:54.209; most accessible tissue: Minghui63 flag leaf, score: 68.16	N	N	N	N
vg1121302509	C -> DEL	N	N	silent_mutation	Average:54.209; most accessible tissue: Minghui63 flag leaf, score: 68.16	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121302509	3.30E-06	2.87E-09	mr1188	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
vg1121302509	NA	1.77E-07	mr1188_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251