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Detailed information for vg1000624564:

Variant ID: vg1000624564 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 624564
Reference Allele: G	Alternative Allele: C,A
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGCTAAGTTCAACAATAGTTTAATTATCTCGTTCGTACACGTTTCGCTCGCGTTCGTTCGCGTTCGTTCACGTTCGTTCGCGTTTCGTTCACGTTCGTTC[G/C,A]
TGTTCGTTCACGTTTCGTTCATGTTCGTTCACGTTTCGTTCGCGTTTCAATCACGTTCGTTTACGTCGTTCGCATTCGTTCACGTTTCGTTCGCGTTCGT

Reverse complement sequence

ACGAACGCGAACGAAACGTGAACGAATGCGAACGACGTAAACGAACGTGATTGAAACGCGAACGAAACGTGAACGAACATGAACGAAACGTGAACGAACA[C/G,T]
GAACGAACGTGAACGAAACGCGAACGAACGTGAACGAACGCGAACGAACGCGAGCGAAACGTGTACGAACGAGATAATTAAACTATTGTTGAACTTAGCA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.70%	12.80%	6.03%	19.47%	A: 0.04%
All Indica	2759	72.90%	1.90%	7.97%	17.14%	A: 0.04%
All Japonica	1512	44.10%	24.30%	3.64%	27.91%	NA
Aus	269	49.80%	47.20%	0.74%	2.23%	NA
Indica I	595	55.50%	0.20%	6.05%	38.32%	NA
Indica II	465	94.20%	0.90%	1.29%	3.66%	NA
Indica III	913	71.30%	3.50%	14.79%	10.41%	NA
Indica Intermediate	786	75.40%	2.00%	5.47%	16.92%	A: 0.13%
Temperate Japonica	767	13.00%	33.60%	6.13%	47.20%	NA
Tropical Japonica	504	89.30%	6.20%	1.19%	3.37%	NA
Japonica Intermediate	241	48.50%	32.80%	0.83%	17.84%	NA
VI/Aromatic	96	47.90%	37.50%	3.12%	10.42%	A: 1.04%
Intermediate	90	61.10%	23.30%	5.56%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000624564	G -> C	LOC_Os10g01984.1	intron_variant ; MODIFIER	silent_mutation	Average:21.366; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg1000624564	G -> A	LOC_Os10g01984.1	intron_variant ; MODIFIER	silent_mutation	Average:21.366; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg1000624564	G -> DEL	N	N	silent_mutation	Average:21.366; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000624564	2.49E-06	NA	mr1002	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
vg1000624564	6.98E-17	4.53E-33	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
vg1000624564	4.97E-10	2.17E-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
vg1000624564	1.37E-18	4.15E-45	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
vg1000624564	4.49E-11	1.13E-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
vg1000624564	NA	2.83E-09	mr1457	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
vg1000624564	NA	2.18E-06	mr1548	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
vg1000624564	NA	4.10E-06	mr1912	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
vg1000624564	7.87E-24	8.59E-59	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
vg1000624564	9.93E-12	5.17E-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
vg1000624564	8.26E-10	9.90E-14	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
vg1000624564	9.47E-09	6.50E-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
vg1000624564	7.57E-28	3.74E-50	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
vg1000624564	4.45E-17	1.13E-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
vg1000624564	2.08E-13	1.64E-22	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
vg1000624564	9.70E-10	2.79E-16	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