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Detailed information for vg1010998659:

Variant ID: vg1010998659 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 10998659
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGATAGCATCTGGTGAAAATTTTTGTAATGTATAGGCATCATCAGAAGTGCTATGAGTGGGACCCATCAAGGTTAATAAAAGAAAGGCAAAATTTGCTA[C/T]
AGGACATCGAAAAAACGTGTAATTAGCTCCTGGACACTCGAGGCCTTATTTTAATATTTCCTATGAACTTGGAGAGAGAAACACTGGTGAGAGTACGATT

Reverse complement sequence

AATCGTACTCTCACCAGTGTTTCTCTCTCCAAGTTCATAGGAAATATTAAAATAAGGCCTCGAGTGTCCAGGAGCTAATTACACGTTTTTTCGATGTCCT[G/A]
TAGCAAATTTTGCCTTTCTTTTATTAACCTTGATGGGTCCCACTCATAGCACTTCTGATGATGCCTATACATTACAAAAATTTTCACCAGATGCTATCCG

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	49.60%	10.00%	0.15%	40.27%	NA
All Indica	2759	28.10%	3.90%	0.18%	67.81%	NA
All Japonica	1512	98.50%	0.70%	0.07%	0.73%	NA
Aus	269	2.60%	97.00%	0.00%	0.37%	NA
Indica I	595	24.00%	2.50%	0.50%	72.94%	NA
Indica II	465	14.60%	1.10%	0.22%	84.09%	NA
Indica III	913	37.00%	3.10%	0.00%	59.91%	NA
Indica Intermediate	786	28.80%	7.60%	0.13%	63.49%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	98.20%	0.40%	0.20%	1.19%	NA
Japonica Intermediate	241	95.40%	3.30%	0.00%	1.24%	NA
VI/Aromatic	96	17.70%	81.20%	0.00%	1.04%	NA
Intermediate	90	58.90%	18.90%	1.11%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1010998659	C -> T	LOC_Os10g21470.1	upstream_gene_variant ; 1274.0bp to feature; MODIFIER	silent_mutation	Average:12.973; most accessible tissue: Callus, score: 37.163	N	N	N	N
vg1010998659	C -> T	LOC_Os10g21470.2	upstream_gene_variant ; 1274.0bp to feature; MODIFIER	silent_mutation	Average:12.973; most accessible tissue: Callus, score: 37.163	N	N	N	N
vg1010998659	C -> T	LOC_Os10g21479.1	downstream_gene_variant ; 4395.0bp to feature; MODIFIER	silent_mutation	Average:12.973; most accessible tissue: Callus, score: 37.163	N	N	N	N
vg1010998659	C -> T	LOC_Os10g21470-LOC_Os10g21479	intergenic_region ; MODIFIER	silent_mutation	Average:12.973; most accessible tissue: Callus, score: 37.163	N	N	N	N
vg1010998659	C -> DEL	N	N	silent_mutation	Average:12.973; most accessible tissue: Callus, score: 37.163	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1010998659	NA	5.21E-22	mr1095	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
vg1010998659	NA	2.79E-25	mr1210	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
vg1010998659	NA	1.38E-13	mr1231	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
vg1010998659	1.67E-06	NA	mr1246	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
vg1010998659	NA	8.91E-30	mr1305	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
vg1010998659	NA	1.83E-11	mr1409	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
vg1010998659	NA	6.75E-14	mr1522	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
vg1010998659	NA	9.71E-11	mr1585	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
vg1010998659	NA	1.33E-28	mr1586	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
vg1010998659	NA	1.26E-19	mr1765	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
vg1010998659	NA	1.48E-18	mr1911	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
vg1010998659	NA	7.55E-23	mr1961	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
vg1010998659	NA	1.57E-20	mr1095_2	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
vg1010998659	NA	1.77E-07	mr1126_2	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
vg1010998659	NA	3.70E-09	mr1166_2	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
vg1010998659	NA	3.87E-26	mr1305_2	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
vg1010998659	NA	1.15E-11	mr1409_2	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
vg1010998659	NA	7.64E-07	mr1522_2	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
vg1010998659	NA	9.25E-14	mr1583_2	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
vg1010998659	NA	1.65E-08	mr1585_2	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
vg1010998659	NA	4.21E-09	mr1707_2	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
vg1010998659	NA	1.09E-12	mr1803_2	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
vg1010998659	NA	1.91E-15	mr1911_2	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
vg1010998659	NA	1.09E-09	mr1942_2	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