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Detailed information for vg1020215571:

Variant ID: vg1020215571 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 20215571
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACAGACCGGTCAGATTGCGGGTTAGGTGGCGACAGGCGGTCTGACGCACGCCTCGCCCCATCCCGTCAGGACGAGAGCCTCCAAGCACTCGTCCCTAGC[T/C]
GGAGCCGGCGTGTTAGCTCCTGGAGATGGCACGTTGGTTCCGGTATATGCCAGGCTTCATCCTAACCATTACAAGCAAGATATTGTATGAAGAGGGGCGA

Reverse complement sequence

TCGCCCCTCTTCATACAATATCTTGCTTGTAATGGTTAGGATGAAGCCTGGCATATACCGGAACCAACGTGCCATCTCCAGGAGCTAACACGCCGGCTCC[A/G]
GCTAGGGACGAGTGCTTGGAGGCTCTCGTCCTGACGGGATGGGGCGAGGCGTGCGTCAGACCGCCTGTCGCCACCTAACCCGCAATCTGACCGGTCTGTG

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	30.80%	0.20%	1.50%	67.48%	NA
All Indica	2759	2.00%	0.30%	2.21%	95.51%	NA
All Japonica	1512	89.70%	0.00%	0.20%	10.05%	NA
Aus	269	2.20%	0.40%	0.74%	96.65%	NA
Indica I	595	2.90%	0.70%	1.68%	94.79%	NA
Indica II	465	1.50%	0.20%	1.72%	96.56%	NA
Indica III	913	1.40%	0.00%	2.08%	96.50%	NA
Indica Intermediate	786	2.40%	0.30%	3.05%	94.27%	NA
Temperate Japonica	767	97.50%	0.00%	0.13%	2.35%	NA
Tropical Japonica	504	76.40%	0.00%	0.40%	23.21%	NA
Japonica Intermediate	241	92.90%	0.00%	0.00%	7.05%	NA
VI/Aromatic	96	5.20%	0.00%	1.04%	93.75%	NA
Intermediate	90	36.70%	1.10%	4.44%	57.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1020215571	T -> C	LOC_Os10g37770.1	upstream_gene_variant ; 1284.0bp to feature; MODIFIER	silent_mutation	Average:13.077; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg1020215571	T -> C	LOC_Os10g37780.1	downstream_gene_variant ; 3019.0bp to feature; MODIFIER	silent_mutation	Average:13.077; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg1020215571	T -> C	LOC_Os10g37770-LOC_Os10g37780	intergenic_region ; MODIFIER	silent_mutation	Average:13.077; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg1020215571	T -> DEL	N	N	silent_mutation	Average:13.077; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1020215571	NA	1.13E-07	mr1129	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
vg1020215571	NA	1.14E-18	mr1133	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
vg1020215571	NA	2.85E-07	mr1243	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
vg1020215571	NA	2.73E-06	mr1558	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
vg1020215571	NA	3.01E-06	mr1039_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
vg1020215571	NA	4.67E-17	mr1133_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
vg1020215571	NA	1.14E-06	mr1275_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
vg1020215571	NA	1.20E-07	mr1399_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
vg1020215571	NA	7.34E-07	mr1509_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
vg1020215571	NA	2.47E-06	mr1557_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
vg1020215571	2.27E-06	2.38E-13	mr1558_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
vg1020215571	NA	4.52E-15	mr1575_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
vg1020215571	NA	5.24E-06	mr1623_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
vg1020215571	NA	5.23E-08	mr1632_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
vg1020215571	2.50E-06	1.74E-13	mr1667_2	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