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Detailed information for vg1000501724:

Variant ID: vg1000501724 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 501724
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAAAGTGATTTAATTTTAATTGGAAGAGATGACTTAGTGTTAAGAATATGTGAGATAGTTTGTGTGAATGCTAGCGAAAAAGATTAAGTAAATAATAAA[T/C]
ATGTAAATATTTAGTTGTACTAAACTAGCCTTGCATCGCGGATCTGTAATGTCCTTTTTAAGCTCTTAGCGTTTCTGGACTTAGGACGTATAGTAGTGAC

Reverse complement sequence

GTCACTACTATACGTCCTAAGTCCAGAAACGCTAAGAGCTTAAAAAGGACATTACAGATCCGCGATGCAAGGCTAGTTTAGTACAACTAAATATTTACAT[A/G]
TTTATTATTTACTTAATCTTTTTCGCTAGCATTCACACAAACTATCTCACATATTCTTAACACTAAGTCATCTCTTCCAATTAAAATTAAATCACTTTTT

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	79.00%	13.30%	0.80%	6.88%	NA
All Indica	2759	96.00%	0.30%	0.18%	3.52%	NA
All Japonica	1512	58.30%	39.40%	1.79%	0.53%	NA
Aus	269	35.70%	0.70%	1.12%	62.45%	NA
Indica I	595	99.30%	0.30%	0.34%	0.00%	NA
Indica II	465	98.70%	0.40%	0.22%	0.65%	NA
Indica III	913	94.00%	0.10%	0.00%	5.91%	NA
Indica Intermediate	786	94.10%	0.50%	0.25%	5.09%	NA
Temperate Japonica	767	24.80%	72.60%	2.48%	0.13%	NA
Tropical Japonica	504	97.20%	2.60%	0.20%	0.00%	NA
Japonica Intermediate	241	83.40%	10.80%	2.90%	2.90%	NA
VI/Aromatic	96	46.90%	9.40%	0.00%	43.75%	NA
Intermediate	90	71.10%	14.40%	3.33%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000501724	T -> C	LOC_Os10g01770.1	intron_variant ; MODIFIER	silent_mutation	Average:25.61; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg1000501724	T -> DEL	N	N	silent_mutation	Average:25.61; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000501724	NA	4.51E-06	mr1026	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
vg1000501724	3.69E-20	7.25E-41	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
vg1000501724	4.68E-10	2.99E-14	mr1300	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
vg1000501724	5.73E-24	6.95E-61	mr1310	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
vg1000501724	6.97E-11	1.05E-17	mr1310	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
vg1000501724	4.18E-09	2.59E-08	mr1498	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
vg1000501724	2.18E-31	9.43E-73	mr1926	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
vg1000501724	9.67E-13	1.56E-20	mr1926	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
vg1000501724	2.48E-14	2.38E-20	mr1959	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
vg1000501724	5.62E-09	3.54E-11	mr1959	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
vg1000501724	NA	1.90E-06	mr1195_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
vg1000501724	3.51E-36	2.99E-70	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
vg1000501724	6.74E-17	3.68E-27	mr1310_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
vg1000501724	1.35E-20	3.80E-32	mr1959_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
vg1000501724	1.71E-11	1.11E-18	mr1959_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