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Detailed information for vg1023002650:

Variant ID: vg1023002650 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 23002650
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGGTGGCTTGCCTTGCTCGAGATCTGGAGCTTGATCCTCGAAATCCTCGCACTGCGGGTCTTCGGGCTCCGGAACTACACGCGAAATGGGACAACTCAA[C/T]
AAACGGCGAAAATAAAGCCCTATTAATGACCTCTAAGCGTGCCATTAGATAGATCTCGAGATTTGGGGAATTTTGGAAGTTGAACGGAGTCAAACGGATT

Reverse complement sequence

AATCCGTTTGACTCCGTTCAACTTCCAAAATTCCCCAAATCTCGAGATCTATCTAATGGCACGCTTAGAGGTCATTAATAGGGCTTTATTTTCGCCGTTT[G/A]
TTGAGTTGTCCCATTTCGCGTGTAGTTCCGGAGCCCGAAGACCCGCAGTGCGAGGATTTCGAGGATCAAGCTCCAGATCTCGAGCAAGGCAAGCCACCTT

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	33.30%	2.90%	4.53%	59.27%	NA
All Indica	2759	4.70%	0.00%	5.47%	89.85%	NA
All Japonica	1512	86.60%	8.70%	1.52%	3.17%	NA
Aus	269	3.70%	0.00%	12.27%	84.01%	NA
Indica I	595	4.90%	0.00%	2.52%	92.61%	NA
Indica II	465	5.40%	0.00%	6.24%	88.39%	NA
Indica III	913	2.60%	0.00%	5.91%	91.46%	NA
Indica Intermediate	786	6.50%	0.00%	6.74%	86.77%	NA
Temperate Japonica	767	94.40%	4.00%	0.65%	0.91%	NA
Tropical Japonica	504	74.80%	13.90%	3.37%	7.94%	NA
Japonica Intermediate	241	86.70%	12.40%	0.41%	0.41%	NA
VI/Aromatic	96	81.20%	5.20%	2.08%	11.46%	NA
Intermediate	90	51.10%	2.20%	5.56%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1023002650	C -> T	LOC_Os10g42650.1	upstream_gene_variant ; 3518.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1023002650	C -> T	LOC_Os10g42660.1	downstream_gene_variant ; 2897.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1023002650	C -> T	LOC_Os10g42650-LOC_Os10g42660	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1023002650	C -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1023002650	1.05E-06	1.05E-06	mr1367_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