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Detailed information for vg1013488546:

Variant ID: vg1013488546 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 13488546
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGCGCCATGAAGCAAACATCGGAGATGTTCTTTCCCTTATCATCATCTCCACTCTCACCATCTACATCACTTAGTGGCTCGAAGGCGGCGCAAACTTGTT[G/C]
AAAAGCCTTCCTGAGATTCTCCATCTTCCTCCCTTGGTATGAACCCTTCGGCTTGTTGTTGTTGTTCTTCTCACCATCTTTGTCTTCTCTTTTGCCTCTC

Reverse complement sequence

GAGAGGCAAAAGAGAAGACAAAGATGGTGAGAAGAACAACAACAACAAGCCGAAGGGTTCATACCAAGGGAGGAAGATGGAGAATCTCAGGAAGGCTTTT[C/G]
AACAAGTTTGCGCCGCCTTCGAGCCACTAAGTGATGTAGATGGTGAGAGTGGAGATGATGATAAGGGAAAGAACATCTCCGATGTTTGCTTCATGGCGCG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.50%	8.50%	0.00%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	74.30%	25.70%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	94.70%	5.30%	0.00%	0.00%	NA
Tropical Japonica	504	51.40%	48.60%	0.00%	0.00%	NA
Japonica Intermediate	241	57.30%	42.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1013488546	G -> C	LOC_Os10g26040.1	missense_variant ; p.Gln197Glu; MODERATE	nonsynonymous_codon ; Q197E	Average:24.981; most accessible tissue: Minghui63 young leaf, score: 39.381	benign	0.958	TOLERATED	0.23

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1013488546	NA	2.27E-07	mr1248	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
vg1013488546	2.13E-06	NA	mr1533	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
vg1013488546	NA	1.96E-13	mr1533	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
vg1013488546	NA	6.04E-31	mr1699	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
vg1013488546	1.13E-09	NA	mr1980	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
vg1013488546	1.69E-06	1.86E-19	mr1980	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
vg1013488546	NA	1.31E-06	mr1422_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
vg1013488546	2.05E-15	NA	mr1533_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
vg1013488546	1.98E-14	1.79E-28	mr1533_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
vg1013488546	NA	5.65E-07	mr1554_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
vg1013488546	4.93E-06	4.93E-06	mr1610_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
vg1013488546	NA	6.28E-10	mr1819_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
vg1013488546	1.09E-09	NA	mr1980_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
vg1013488546	9.00E-07	1.27E-11	mr1980_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