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Detailed information for vg0123436071:

Variant ID: vg0123436071 (JBrowse)	Variation Type: INDEL
Chromosome: chr01	Position: 23436071
Reference Allele: TGGTTGAAATAACCGGAACTAAAGATACATCTTTAGTCCC	Alternative Allele: CGGTTGAAATAACCGGAACTAAAGATACATCTTTAGTCCC,T
Primary Allele: CGGTTGAAATAACCGGAACT AAAGATACATCTTTAGTCCC	Secondary Allele: TGGTTGAAATAACCGGAACT AAAGATACATCTTTAGTCCC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTGGAGAAAGGATTTGTAGTCCCGATTGGTAACCCTCTGTAGTCCCGGTTTTTCAACCGGGACTACGAATCTGGGACTAAAGATGTCCATCTTTAGTCC[TGGTTGAAATAACCGGAACTAAAGATACATCTTTAGTCCC/CGGTTGAAATAACCGGAACTAAAGATACATCTTTAGTCCC,T]
GGTTCGTAACACCAACCAGGACTAAAGATTTAGTCCCGGTTGATGTAACCAACCGGGACTAAAGTTTTTTTTTTTCTTTTTTTTCTTTTCTCATGTTCAA

Reverse complement sequence

TTGAACATGAGAAAAGAAAAAAAAGAAAAAAAAAAACTTTAGTCCCGGTTGGTTACATCAACCGGGACTAAATCTTTAGTCCTGGTTGGTGTTACGAACC[GGGACTAAAGATGTATCTTTAGTTCCGGTTATTTCAACCA/GGGACTAAAGATGTATCTTTAGTTCCGGTTATTTCAACCG,A]
GGACTAAAGATGGACATCTTTAGTCCCAGATTCGTAGTCCCGGTTGAAAAACCGGGACTACAGAGGGTTACCAATCGGGACTACAAATCCTTTCTCCACC

Allele Frequencies:

Populations	Population Size	Frequency of CGGTTGAAATAACCGGAACT AAAGATACATCTTTAGTCCC(primary allele)	Frequency of TGGTTGAAATAACCGGAACT AAAGATACATCTTTAGTCCC(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.40%	27.20%	3.05%	14.07%	T: 2.26%
All Indica	2759	79.90%	11.30%	3.04%	1.96%	T: 3.77%
All Japonica	1512	14.40%	44.80%	3.44%	37.30%	NA
Aus	269	5.60%	93.30%	0.37%	0.37%	T: 0.37%
Indica I	595	92.30%	0.30%	2.35%	0.67%	T: 4.37%
Indica II	465	94.00%	3.20%	0.65%	1.51%	T: 0.65%
Indica III	913	64.00%	23.90%	4.49%	2.63%	T: 5.04%
Indica Intermediate	786	80.80%	9.80%	3.31%	2.42%	T: 3.69%
Temperate Japonica	767	0.40%	63.60%	0.52%	35.46%	NA
Tropical Japonica	504	30.40%	10.50%	7.54%	51.59%	NA
Japonica Intermediate	241	25.70%	56.80%	4.15%	13.28%	NA
VI/Aromatic	96	49.00%	16.70%	3.12%	31.25%	NA
Intermediate	90	42.20%	33.30%	4.44%	17.78%	T: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0123436071	TGGTTGAAATAACCGGAACTAAAGATACATCTTTAGTCCC -> CGGTTGAAATAACCGGAACTAAAGATACAT CTTTAGTCCC	LOC_Os01g41400.1	upstream_gene_variant ; 3438.0bp to feature; MODIFIER	silent_mutation	Average:43.133; most accessible tissue: Zhenshan97 root, score: 59.664	N	N	N	N
vg0123436071	TGGTTGAAATAACCGGAACTAAAGATACATCTTTAGTCCC -> CGGTTGAAATAACCGGAACTAAAGATACAT CTTTAGTCCC	LOC_Os01g41390-LOC_Os01g41400	intergenic_region ; MODIFIER	silent_mutation	Average:43.133; most accessible tissue: Zhenshan97 root, score: 59.664	N	N	N	N
vg0123436071	TGGTTGAAATAACCGGAACTAAAGATACATCTTTAGTCCC -> T	LOC_Os01g41400.1	upstream_gene_variant ; 3437.0bp to feature; MODIFIER	silent_mutation	Average:43.133; most accessible tissue: Zhenshan97 root, score: 59.664	N	N	N	N
vg0123436071	TGGTTGAAATAACCGGAACTAAAGATACATCTTTAGTCCC -> T	LOC_Os01g41390-LOC_Os01g41400	intergenic_region ; MODIFIER	silent_mutation	Average:43.133; most accessible tissue: Zhenshan97 root, score: 59.664	N	N	N	N
vg0123436071	TGGTTGAAATAACCGGAACTAAAGATACATCTTTAGTCCC -> DEL	N	N	silent_mutation	Average:43.133; most accessible tissue: Zhenshan97 root, score: 59.664	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0123436071	NA	2.53E-06	mr1030	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
vg0123436071	NA	4.89E-09	mr1045	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
vg0123436071	NA	1.87E-06	mr1126	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
vg0123436071	NA	4.70E-17	mr1147	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
vg0123436071	NA	7.42E-06	mr1149	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
vg0123436071	NA	8.57E-07	mr1157	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
vg0123436071	NA	2.81E-06	mr1202	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
vg0123436071	NA	2.47E-06	mr1271	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
vg0123436071	5.86E-06	4.09E-07	mr1387	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
vg0123436071	NA	1.39E-06	mr1440	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
vg0123436071	NA	3.97E-06	mr1441	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
vg0123436071	3.38E-06	3.37E-06	mr1452	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
vg0123436071	8.42E-07	1.82E-07	mr1513	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
vg0123436071	NA	5.04E-12	mr1540	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
vg0123436071	NA	3.73E-06	mr1576	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
vg0123436071	9.26E-07	8.12E-06	mr1590	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
vg0123436071	NA	6.01E-06	mr1596	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
vg0123436071	NA	9.73E-06	mr1614	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
vg0123436071	3.59E-06	NA	mr1630	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
vg0123436071	NA	2.84E-08	mr1666	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
vg0123436071	8.04E-06	8.03E-06	mr1694	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
vg0123436071	NA	1.12E-10	mr1712	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
vg0123436071	NA	6.63E-06	mr1738	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
vg0123436071	NA	2.32E-10	mr1748	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
vg0123436071	NA	1.07E-06	mr1837	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
vg0123436071	NA	1.06E-06	mr1875	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
vg0123436071	NA	1.94E-06	mr1880	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
vg0123436071	NA	9.89E-07	mr1941	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
vg0123436071	NA	4.42E-08	mr1137_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