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Detailed information for vg1000256952:

Variant ID: vg1000256952 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 256952
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCATGACAACGTCATGCTCTCCTGCGGCCGGCCTCTCTTGCACCATCCACGATAGGGTGGCATCAATGCGGGTGAGCTAGGCAGGGGCGGAGCCAGAAT[A/T]
AAACAAGGGGGTTTCACTCGTTTGCTTTACTCTGGTTTAAATCAAATTTAGCTTGATACGGGTGCATAAAATTAAACTAACGGGTATATATATGGTGAAA

Reverse complement sequence

TTTCACCATATATATACCCGTTAGTTTAATTTTATGCACCCGTATCAAGCTAAATTTGATTTAAACCAGAGTAAAGCAAACGAGTGAAACCCCCTTGTTT[T/A]
ATTCTGGCTCCGCCCCTGCCTAGCTCACCCGCATTGATGCCACCCTATCGTGGATGGTGCAAGAGAGGCCGGCCGCAGGAGAGCATGACGTTGTCATGGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.10%	2.40%	0.06%	16.48%	NA
All Indica	2759	98.70%	0.00%	0.00%	1.23%	NA
All Japonica	1512	56.90%	6.70%	0.20%	36.11%	NA
Aus	269	54.30%	0.00%	0.00%	45.72%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	97.60%	0.20%	0.00%	2.15%	NA
Indica III	913	99.90%	0.00%	0.00%	0.11%	NA
Indica Intermediate	786	97.10%	0.00%	0.00%	2.93%	NA
Temperate Japonica	767	77.10%	12.80%	0.13%	10.04%	NA
Tropical Japonica	504	25.60%	0.00%	0.40%	74.01%	NA
Japonica Intermediate	241	58.50%	1.70%	0.00%	39.83%	NA
VI/Aromatic	96	32.30%	9.40%	0.00%	58.33%	NA
Intermediate	90	76.70%	1.10%	0.00%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000256952	A -> T	LOC_Os10g01420.1	upstream_gene_variant ; 3935.0bp to feature; MODIFIER	silent_mutation	Average:11.182; most accessible tissue: Callus, score: 36.429	N	N	N	N
vg1000256952	A -> T	LOC_Os10g01430.1	upstream_gene_variant ; 3042.0bp to feature; MODIFIER	silent_mutation	Average:11.182; most accessible tissue: Callus, score: 36.429	N	N	N	N
vg1000256952	A -> T	LOC_Os10g01420-LOC_Os10g01430	intergenic_region ; MODIFIER	silent_mutation	Average:11.182; most accessible tissue: Callus, score: 36.429	N	N	N	N
vg1000256952	A -> DEL	N	N	silent_mutation	Average:11.182; most accessible tissue: Callus, score: 36.429	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000256952	5.73E-08	5.73E-08	mr1038	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
vg1000256952	1.18E-06	1.18E-06	mr1343	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
vg1000256952	NA	9.99E-08	mr1354	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
vg1000256952	6.40E-07	6.40E-07	mr1389	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
vg1000256952	NA	1.71E-08	mr1829	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
vg1000256952	NA	1.95E-06	mr1902	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
vg1000256952	7.10E-07	5.48E-10	mr1038_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
vg1000256952	NA	1.02E-10	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
vg1000256952	7.63E-10	7.63E-10	mr1389_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
vg1000256952	NA	3.35E-06	mr1549_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
vg1000256952	NA	6.04E-06	mr1757_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
vg1000256952	NA	1.69E-06	mr1829_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
vg1000256952	NA	5.83E-06	mr1902_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