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Detailed information for vg1107147822:

Variant ID: vg1107147822 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 7147822
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAAAATCAATTCCCTATCATTTGTTAGTTTGCCACGTAAGCAAGGTGAGGCCCAGTTCGGTACTTGTGCACGTCTTCTCCCTCCCGCACCAGCGCCGAT[C/T]
GACTTCTTCCTCCCCGGACCTGCGCCGCCGTGACCTAGCGCCATCATCACCAGCCAGTCAACCAGTGTCCTGACTGCTGCGATTTGTTAAAAAACGGAAC

Reverse complement sequence

GTTCCGTTTTTTAACAAATCGCAGCAGTCAGGACACTGGTTGACTGGCTGGTGATGATGGCGCTAGGTCACGGCGGCGCAGGTCCGGGGAGGAAGAAGTC[G/A]
ATCGGCGCTGGTGCGGGAGGGAGAAGACGTGCACAAGTACCGAACTGGGCCTCACCTTGCTTACGTGGCAAACTAACAAATGATAGGGAATTGATTTTTG

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	42.20%	2.80%	8.61%	46.32%	NA
All Indica	2759	54.50%	0.70%	7.76%	37.04%	NA
All Japonica	1512	14.90%	5.80%	9.26%	70.04%	NA
Aus	269	75.80%	2.20%	7.06%	14.87%	NA
Indica I	595	80.80%	0.00%	1.18%	17.98%	NA
Indica II	465	26.20%	2.60%	11.40%	59.78%	NA
Indica III	913	51.00%	0.00%	12.16%	36.80%	NA
Indica Intermediate	786	55.50%	0.80%	5.47%	38.30%	NA
Temperate Japonica	767	20.60%	0.40%	6.52%	72.49%	NA
Tropical Japonica	504	5.20%	12.30%	15.28%	67.26%	NA
Japonica Intermediate	241	17.00%	9.50%	5.39%	68.05%	NA
VI/Aromatic	96	14.60%	21.90%	25.00%	38.54%	NA
Intermediate	90	53.30%	1.10%	11.11%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1107147822	C -> T	LOC_Os11g12680.1	upstream_gene_variant ; 1590.0bp to feature; MODIFIER	silent_mutation	Average:32.835; most accessible tissue: Zhenshan97 root, score: 79.71	N	N	N	N
vg1107147822	C -> T	LOC_Os11g12670-LOC_Os11g12680	intergenic_region ; MODIFIER	silent_mutation	Average:32.835; most accessible tissue: Zhenshan97 root, score: 79.71	N	N	N	N
vg1107147822	C -> DEL	N	N	silent_mutation	Average:32.835; most accessible tissue: Zhenshan97 root, score: 79.71	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1107147822	5.04E-06	5.04E-06	mr1266	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
vg1107147822	6.85E-07	6.84E-07	mr1655	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