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Detailed information for vg1122960079:

Variant ID: vg1122960079 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22960079
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGAAAAAAAATCCACGTTACCATCTTTCTTCTTTCGGTGTTATAATTTATATATAAAGTTTCTGGTGATTTATACATTTTTTTATTTAAAAACCAAAACA[T/C]
ATTTTTTTTAGAATTACACAGTACAACACAGACACTCACAACGCACGTACGCAAACCCTACCCCTATGAGCATCTTCGAAGATTGGGCTGGCAAATCCTG

Reverse complement sequence

CAGGATTTGCCAGCCCAATCTTCGAAGATGCTCATAGGGGTAGGGTTTGCGTACGTGCGTTGTGAGTGTCTGTGTTGTACTGTGTAATTCTAAAAAAAAT[A/G]
TGTTTTGGTTTTTAAATAAAAAAATGTATAAATCACCAGAAACTTTATATATAAATTATAACACCGAAAGAAGAAAGATGGTAACGTGGATTTTTTTTCT

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	79.10%	18.20%	0.13%	2.56%	NA
All Indica	2759	88.00%	11.80%	0.07%	0.11%	NA
All Japonica	1512	59.10%	32.90%	0.20%	7.80%	NA
Aus	269	95.20%	4.80%	0.00%	0.00%	NA
Indica I	595	94.50%	5.50%	0.00%	0.00%	NA
Indica II	465	97.20%	2.60%	0.00%	0.22%	NA
Indica III	913	76.70%	23.10%	0.22%	0.00%	NA
Indica Intermediate	786	90.80%	8.90%	0.00%	0.25%	NA
Temperate Japonica	767	42.00%	55.10%	0.13%	2.74%	NA
Tropical Japonica	504	76.00%	7.70%	0.20%	16.07%	NA
Japonica Intermediate	241	78.40%	14.50%	0.41%	6.64%	NA
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	82.20%	16.70%	1.11%	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
vg1122960079	T -> DEL	N	N	silent_mutation	Average:40.022; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg1122960079	T -> C	LOC_Os11g38680.1	downstream_gene_variant ; 1952.0bp to feature; MODIFIER	silent_mutation	Average:40.022; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg1122960079	T -> C	LOC_Os11g38690.1	downstream_gene_variant ; 1967.0bp to feature; MODIFIER	silent_mutation	Average:40.022; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg1122960079	T -> C	LOC_Os11g38680-LOC_Os11g38690	intergenic_region ; MODIFIER	silent_mutation	Average:40.022; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122960079	NA	7.66E-07	mr1138_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
vg1122960079	NA	2.63E-08	mr1156_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
vg1122960079	NA	8.31E-07	mr1354_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
vg1122960079	1.82E-06	1.82E-06	mr1579_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
vg1122960079	NA	1.33E-06	mr1621_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
vg1122960079	NA	3.20E-07	mr1980_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