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Detailed information for vg0715275897:

Variant ID: vg0715275897 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15275897
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAGTTCCATTTACGTAATAAGGTTGATAATTTTAAGTAGGGTTTAGTTTTGGTGTATGATCCTGCACAAAATGAGTTTAAGGATCAATTCCTTGCTGAA[T/C]
TAGTTAATATGTGCAGTCATGAGACCTTACCAATTCTTATTGGTGGTGATTTTAATATTCTTCGTAGCCCTAATGAGAAAAATAATGATAATTTTGATGA

Reverse complement sequence

TCATCAAAATTATCATTATTTTTCTCATTAGGGCTACGAAGAATATTAAAATCACCACCAATAAGAATTGGTAAGGTCTCATGACTGCACATATTAACTA[A/G]
TTCAGCAAGGAATTGATCCTTAAACTCATTTTGTGCAGGATCATACACCAAAACTAAACCCTACTTAAAATTATCAACCTTATTACGTAAATGGAACTTA

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	90.20%	5.40%	1.33%	3.03%	NA
All Indica	2759	98.30%	0.20%	0.29%	1.27%	NA
All Japonica	1512	78.60%	13.50%	3.04%	4.89%	NA
Aus	269	95.90%	0.00%	1.49%	2.60%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.10%	0.60%	0.22%	0.00%	NA
Indica III	913	99.80%	0.00%	0.11%	0.11%	NA
Indica Intermediate	786	94.70%	0.30%	0.76%	4.33%	NA
Temperate Japonica	767	84.60%	3.30%	2.74%	9.39%	NA
Tropical Japonica	504	72.40%	25.40%	2.18%	0.00%	NA
Japonica Intermediate	241	72.20%	21.20%	5.81%	0.83%	NA
VI/Aromatic	96	32.30%	37.50%	3.12%	27.08%	NA
Intermediate	90	83.30%	13.30%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0715275897	T -> DEL	N	N	silent_mutation	Average:35.303; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0715275897	T -> C	LOC_Os07g26510.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:35.303; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715275897	7.25E-06	NA	mr1104	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
vg0715275897	NA	1.04E-06	mr1104	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
vg0715275897	2.26E-06	NA	mr1107	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
vg0715275897	NA	1.81E-07	mr1213	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
vg0715275897	2.43E-07	NA	mr1226	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
vg0715275897	4.26E-06	NA	mr1301	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
vg0715275897	NA	1.97E-08	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
vg0715275897	5.60E-06	1.53E-07	mr1602	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
vg0715275897	NA	1.91E-06	mr1602	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
vg0715275897	1.49E-06	NA	mr1082_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
vg0715275897	2.86E-06	NA	mr1083_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
vg0715275897	2.50E-06	NA	mr1085_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
vg0715275897	8.53E-11	NA	mr1104_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
vg0715275897	4.00E-06	7.95E-08	mr1104_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
vg0715275897	1.45E-09	NA	mr1107_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
vg0715275897	1.36E-06	NA	mr1155_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
vg0715275897	NA	2.67E-07	mr1155_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
vg0715275897	NA	7.04E-06	mr1224_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
vg0715275897	6.30E-08	NA	mr1226_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
vg0715275897	NA	3.36E-06	mr1246_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
vg0715275897	NA	1.50E-06	mr1404_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
vg0715275897	NA	2.80E-06	mr1620_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