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Detailed information for vg1007919865:

Variant ID: vg1007919865 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 7919865
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATGGGGGTTTTAATGCACATTCTGCTTGGAATCCTATTCAGGAATTTCTGGGCGTGACAATGACCTCTGTTCAGAAACACTGTGTCTTACGTGCAGTAA[C/T]
AGCGTTAAAATATAGTTGAAATATAGTCGTGACGGATCTACTTTTGATAAGCTCTTTTTTTCTAGCATCATGGTGCAAACGGTTTTAAAAAACCTTACAT

Reverse complement sequence

ATGTAAGGTTTTTTAAAACCGTTTGCACCATGATGCTAGAAAAAAAGAGCTTATCAAAAGTAGATCCGTCACGACTATATTTCAACTATATTTTAACGCT[G/A]
TTACTGCACGTAAGACACAGTGTTTCTGAACAGAGGTCATTGTCACGCCCAGAAATTCCTGAATAGGATTCCAAGCAGAATGTGCATTAAAACCCCCATC

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	87.70%	5.60%	1.16%	5.59%	NA
All Indica	2759	99.20%	0.00%	0.04%	0.76%	NA
All Japonica	1512	67.10%	16.60%	3.31%	12.96%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.00%	0.22%	NA
Indica III	913	97.90%	0.10%	0.11%	1.86%	NA
Indica Intermediate	786	99.60%	0.00%	0.00%	0.38%	NA
Temperate Japonica	767	62.60%	29.60%	3.13%	4.69%	NA
Tropical Japonica	504	64.70%	2.60%	4.56%	28.17%	NA
Japonica Intermediate	241	86.70%	4.60%	1.24%	7.47%	NA
VI/Aromatic	96	53.10%	8.30%	1.04%	37.50%	NA
Intermediate	90	81.10%	3.30%	3.33%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1007919865	C -> T	LOC_Os10g15100-LOC_Os10g15120	intergenic_region ; MODIFIER	silent_mutation	Average:23.514; most accessible tissue: Minghui63 flag leaf, score: 35.832	N	N	N	N
vg1007919865	C -> DEL	N	N	silent_mutation	Average:23.514; most accessible tissue: Minghui63 flag leaf, score: 35.832	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1007919865	7.31E-06	NA	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
vg1007919865	NA	1.01E-08	mr1210	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
vg1007919865	1.15E-06	NA	mr1300	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
vg1007919865	4.58E-07	NA	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
vg1007919865	NA	1.23E-09	mr1305	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
vg1007919865	3.35E-06	NA	mr1515	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
vg1007919865	NA	2.34E-08	mr1515	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
vg1007919865	8.11E-06	NA	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
vg1007919865	NA	4.14E-10	mr1585	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
vg1007919865	5.41E-06	NA	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
vg1007919865	NA	4.38E-08	mr1586	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
vg1007919865	NA	1.90E-08	mr1624	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
vg1007919865	NA	2.59E-07	mr1765	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
vg1007919865	NA	7.50E-06	mr1788	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
vg1007919865	NA	4.75E-06	mr1922	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
vg1007919865	1.83E-06	1.83E-06	mr1166_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
vg1007919865	7.79E-06	NA	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
vg1007919865	NA	1.48E-09	mr1305_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
vg1007919865	1.12E-06	NA	mr1310_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
vg1007919865	NA	3.43E-07	mr1409_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
vg1007919865	NA	7.59E-08	mr1559_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
vg1007919865	NA	4.63E-07	mr1559_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
vg1007919865	1.71E-08	1.38E-09	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
vg1007919865	2.16E-06	2.72E-13	mr1585_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
vg1007919865	NA	7.64E-06	mr1765_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
vg1007919865	NA	3.99E-06	mr1793_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