DGRPool

GWAS results were computed on dm3 genome.

If you want to make an independent analysis with DGRP2 or PLINK2, you can find here prepared input files for this phenotype: DGRP2 results PLINK2 results

Full results

Phenotype distribution and association to known covariates

Shapiro-Wilk test of normality (p-value=3.009e^-11)
Null Hypothesis is rejected (p<=0.05).
Interpretation: NOT NORMAL distribution of this phenotype

We tested for association of this phenotype with 6 known covariates Huang et al., 2014 using both ANOVA and Kruskal-Wallis association tests.

ANOVA test
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1565 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

We performed a gene enrichment calculation (Fisher's exact test) of all GWAS-associated genes at p < 0.001. Genesets were taken from two database: the Gene Ontology (GO) and the FlyBase phenotypes. GO enrichment FlyBase phenotype enrichment

Variant impact HIGH MODERATE LOW MODIFIER

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2R	4160757	2R_4160757_SNP [dm3] 2R_8273252_SNP [dm6]	A	G	1.670e^-6	0.985	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2R	4160796	2R_4160796_SNP [dm3] 2R_8273291_SNP [dm6]	C	A	1.904e^-6	0.985	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2R	4160845	2R_4160845_SNP [dm3] 2R_8273340_SNP [dm6]	G	T	2.100e^-6	0.985	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2L	14845282	2L_14845282_SNP [dm3] 2L_14845282_SNP [dm6]	A	G	2.119e^-6	0.985	SYNONYMOUS_CODING CG15279
2L	13567487	2L_13567487_SNP [dm3] 2L_13567487_SNP [dm6]	T	C	3.110e^-6	0.985	INTRON kuz
2L	19185700	2L_19185700_SNP [dm3] 2L_19185700_SNP [dm6]	A	C	5.716e^-6	0.985	START_GAINED gammaTub37C UTR_5_PRIME gammaTub37C UPSTREAM pigeon	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2L	13918297	2L_13918297_SNP [dm3] 2L_13918297_SNP [dm6]	C	T	5.937e^-6	0.985	INTRON Ance-3
2R	10886133	2R_10886133_SNP [dm3] 2R_14998628_SNP [dm6]	A	C	6.146e^-6	0.985	INTERGENIC
2L	1885040	2L_1885040_SNP [dm3] 2L_1885040_SNP [dm6]	T	G	6.508e^-6	0.985	START_GAINED CG7337 UTR_5_PRIME CG7337 UPSTREAM CG15358	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_HSA
2R	18335571	2R_18335571_SNP [dm3] 2R_22448066_SNP [dm6]	C	G	6.798e^-6	0.985	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2L	16524081	2L_16524081_SNP [dm3] 2L_16524081_SNP [dm6]	C	G	7.371e^-6	0.985	INTRON CG5953
2L	6109429	2L_6109429_SNP [dm3] 2L_6109429_SNP [dm6]	G	T	7.385e^-6	0.985	UPSTREAM stai INTRON stai	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3L	20060825	3L_20060825_MNP [dm3] 3L_20067725_MNP [dm6]	TGCTTGGC	ATAAAAGG	9.221e^-6	0.985	INTRON sNPF-R
2L	14851226	2L_14851226_SNP [dm3] 2L_14851226_SNP [dm6]	G	A	9.284e^-6	0.985	INTRON CG15279	TF binding site mE1_TFBS_bab1
2L	14845267	2L_14845267_SNP [dm3] 2L_14845267_SNP [dm6]	T	C	9.974e^-6	0.985	SYNONYMOUS_CODING CG15279
2R	10886159	2R_10886159_SNP [dm3] 2R_14998654_SNP [dm6]	A	G	1.014e^-5	0.985	INTERGENIC
3R	22960308	3R_22960308_INS [dm3] 3R_27134586_INS [dm6]	A	ATTGTA	1.024e^-5	0.985	INTRON CG6051
2L	13567489	2L_13567489_SNP [dm3] 2L_13567489_SNP [dm6]	T	A	1.054e^-5	0.985	INTRON kuz
2L	14902005	2L_14902005_SNP [dm3] 2L_14902005_SNP [dm6]	T	C	1.144e^-5	0.985	INTERGENIC
2R	7312312	2R_7312312_SNP [dm3] 2R_11424807_SNP [dm6]	A	C	1.164e^-5	0.985	UPSTREAM Drip INTRON Drip
2L	14873657	2L_14873657_SNP [dm3] 2L_14873657_SNP [dm6]	A	T	1.211e^-5	0.985	DOWNSTREAM CG15278 INTERGENIC
2L	14870398	2L_14870398_SNP [dm3] 2L_14870398_SNP [dm6]	A	G	1.217e^-5	0.985	UTR_3_PRIME CG4480 DOWNSTREAM CG4480
2L	14870400	2L_14870400_SNP [dm3] 2L_14870400_SNP [dm6]	G	C	1.217e^-5	0.985	UTR_3_PRIME CG4480 DOWNSTREAM CG4480
2L	14870293	2L_14870293_SNP [dm3] 2L_14870293_SNP [dm6]	C	T	1.329e^-5	0.989	DOWNSTREAM CG4480 INTERGENIC
2L	6109434	2L_6109434_SNP [dm3] 2L_6109434_SNP [dm6]	T	A	1.341e^-5	0.989	UPSTREAM stai INTRON stai	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2L	4234877	2L_4234877_SNP [dm3] 2L_4234877_SNP [dm6]	T	C	1.382e^-5	0.989	INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	14851832	2L_14851832_SNP [dm3] 2L_14851832_SNP [dm6]	A	T	1.688e^-5	1	UPSTREAM CG15279 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
2L	14902003	2L_14902003_SNP [dm3] 2L_14902003_SNP [dm6]	T	C	1.811e^-5	1	INTERGENIC
2L	14890907	2L_14890907_SNP [dm3] 2L_14890907_SNP [dm6]	C	A	1.886e^-5	1	INTERGENIC
X	1042583	X_1042583_SNP [dm3] X_1148550_SNP [dm6]	C	A	1.981e^-5	1	INTERGENIC
2L	1881274	2L_1881274_SNP [dm3] 2L_1881274_SNP [dm6]	A	C	2.002e^-5	1	UPSTREAM CG31663 DOWNSTREAM CG15358 INTRON CG31663
2R	10986681	2R_10986681_INS [dm3] 2R_15099176_INS [dm6]	A	TCCTTAATTTCC...	2.116e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi
2R	11661653	2R_11661653_SNP [dm3] 2R_15774148_SNP [dm6]	G	C	2.199e^-5	1	INTRON Zasp52	TF binding site mE1_TFBS_chinmo
2L	1881277	2L_1881277_SNP [dm3] 2L_1881277_SNP [dm6]	A	G	2.249e^-5	1	UPSTREAM CG31663 DOWNSTREAM CG15358 INTRON CG31663
2L	11588421	2L_11588421_SNP [dm3] 2L_11588421_SNP [dm6]	C	A	2.302e^-5	1	UPSTREAM CR44496 INTRON kek2
2L	14850807	2L_14850807_SNP [dm3] 2L_14850807_SNP [dm6]	C	A	2.730e^-5	1	INTRON CG15279
2L	2954228	2L_2954228_SNP [dm3] 2L_2954228_SNP [dm6]	A	G	2.738e^-5	1	UTR_3_PRIME lilli UPSTREAM Rbp9	TF binding site BDTNP1_TFBS_twi
2L	1880745	2L_1880745_DEL [dm3] 2L_1880745_DEL [dm6]	TACGCAGAT	T	2.870e^-5	1	UPSTREAM CG31663 INTRON CG31663
2L	14900326	2L_14900326_SNP [dm3] 2L_14900326_SNP [dm6]	G	C	2.929e^-5	1	INTERGENIC
2L	11021766	2L_11021766_SNP [dm3] 2L_11021766_SNP [dm6]	G	T	2.932e^-5	1	INTRON Samuel
2L	11021767	2L_11021767_SNP [dm3] 2L_11021767_SNP [dm6]	C	T	2.932e^-5	1	INTRON Samuel
2L	15742826	2L_15742826_SNP [dm3] 2L_15742826_SNP [dm6]	T	C	3.047e^-5	1	INTRON CycE	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad
2L	11578420	2L_11578420_DEL [dm3] 2L_11578420_DEL [dm6]	TA	T	3.049e^-5	1	INTERGENIC
X	13840540	X_13840540_SNP [dm3] X_13946507_SNP [dm6]	C	T	3.197e^-5	1	INTRON mamo
2L	2311882	2L_2311882_SNP [dm3] 2L_2311882_SNP [dm6]	A	C	3.228e^-5	1	UTR_5_PRIME eys INTRON CG9967	TF binding site mE1_TFBS_Trl
2L	16472709	2L_16472709_SNP [dm3] 2L_16472709_SNP [dm6]	T	G	3.333e^-5	1	INTRON dac	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	10986668	2R_10986668_SNP [dm3] 2R_15099163_SNP [dm6]	T	G	3.392e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi
2L	9737908	2L_9737908_SNP [dm3] 2L_9737908_SNP [dm6]	T	A	3.413e^-5	1	DOWNSTREAM CG13117 INTRON Nckx30C
3L	7299023	3L_7299023_SNP [dm3] 3L_7305923_SNP [dm6]	C	T	3.470e^-5	1	INTRON unc-13-4A
X	10931888	X_10931888_SNP [dm3] X_11037855_SNP [dm6]	C	A	3.668e^-5	1	UPSTREAM CG42339 INTRON CG42339
2R	7276529	2R_7276529_SNP [dm3] 2R_11389024_SNP [dm6]	T	C	3.676e^-5	1	UPSTREAM CG30022 INTRON sprt
2L	11573668	2L_11573668_SNP [dm3] 2L_11573668_SNP [dm6]	T	C	3.744e^-5	1	INTERGENIC
2L	11573570	2L_11573570_SNP [dm3] 2L_11573570_SNP [dm6]	T	C	3.902e^-5	1	INTERGENIC
2L	1880765	2L_1880765_SNP [dm3] 2L_1880765_SNP [dm6]	C	T	3.973e^-5	1	UPSTREAM CG31663 INTRON CG31663
2L	10166838	2L_10166838_SNP [dm3] 2L_10166838_SNP [dm6]	A	C	4.056e^-5	1	INTRON CG44153
2L	11345378	2L_11345378_SNP [dm3] 2L_11345378_SNP [dm6]	G	A	4.199e^-5	1	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_Kr
2L	21824579	2L_21824579_SNP [dm3] 2L_21824579_SNP [dm6]	A	T	4.262e^-5	1	INTERGENIC
2L	15417900	2L_15417900_SNP [dm3] 2L_15417900_SNP [dm6]	A	G	4.312e^-5	1	DOWNSTREAM CG44869 INTERGENIC
2R	7087729	2R_7087729_DEL [dm3] 2R_11200224_DEL [dm6]	AA	A	4.354e^-5	1	INTRON shn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_twi
2R	3492512	2R_3492512_SNP [dm3] 2R_7605007_SNP [dm6]	C	A	4.388e^-5	1	INTRON CG1358	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	14890981	2L_14890981_SNP [dm3] 2L_14890981_SNP [dm6]	G	A	4.538e^-5	1	INTERGENIC
2L	14890985	2L_14890985_SNP [dm3] 2L_14890985_SNP [dm6]	T	C	4.538e^-5	1	INTERGENIC
2L	14890987	2L_14890987_SNP [dm3] 2L_14890987_SNP [dm6]	C	A	4.538e^-5	1	INTERGENIC
3L	19826130	3L_19826130_SNP [dm3] 3L_19833030_SNP [dm6]	C	T	4.562e^-5	1	SYNONYMOUS_CODING trc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3L	2035946	3L_2035946_SNP [dm3] 3L_2035946_SNP [dm6]	T	A	4.594e^-5	1	INTERGENIC
2R	12332584	2R_12332584_SNP [dm3] 2R_16445079_SNP [dm6]	G	A	4.602e^-5	1	UPSTREAM CG15925 DOWNSTREAM CG4409 INTERGENIC
2L	14863041	2L_14863041_SNP [dm3] 2L_14863041_SNP [dm6]	A	C	4.678e^-5	1	INTERGENIC
2L	14890889	2L_14890889_SNP [dm3] 2L_14890889_SNP [dm6]	T	A	4.689e^-5	1	INTERGENIC
2L	1999948	2L_1999948_SNP [dm3] 2L_1999948_SNP [dm6]	A	T	4.748e^-5	1	UPSTREAM CR43464 INTRON CG33543
2L	14801521	2L_14801521_SNP [dm3] 2L_14801521_SNP [dm6]	C	T	4.837e^-5	1	UPSTREAM CG33308 INTERGENIC
2L	1304632	2L_1304632_SNP [dm3] 2L_1304632_SNP [dm6]	G	T	5.000e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	10986689	2R_10986689_SNP [dm3] 2R_15099184_SNP [dm6]	A	T	5.050e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi
2R	19373690	2R_19373690_SNP [dm3] 2R_23486167_SNP [dm6]	A	T	5.226e^-5	1	INTRON CG43795
2L	14890927	2L_14890927_SNP [dm3] 2L_14890927_SNP [dm6]	A	T	5.324e^-5	1	INTERGENIC
X	18233152	X_18233152_SNP [dm3] X_18339119_SNP [dm6]	C	T	5.344e^-5	1	INTRON CG6123
2L	14874897	2L_14874897_INS [dm3] 2L_14874897_INS [dm6]	T	TTTGT	5.546e^-5	1	UTR_3_PRIME CG15278 DOWNSTREAM CG15278
2R	14662713	2R_14662713_SNP [dm3] 2R_18775208_SNP [dm6]	G	T	5.554e^-5	1	UPSTREAM CR43964 DOWNSTREAM Mctp & 1 other INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
X	11111178	X_11111178_SNP [dm3] X_11217145_SNP [dm6]	T	C	5.600e^-5	1	INTERGENIC
2L	5568007	2L_5568007_SNP [dm3] 2L_5568007_SNP [dm6]	C	T	5.601e^-5	1	INTERGENIC
2L	1999943	2L_1999943_DEL [dm3] 2L_1999943_DEL [dm6]	TCA	T	5.735e^-5	1	UPSTREAM CR43464 INTRON CG33543
2L	1671942	2L_1671942_SNP [dm3] 2L_1671942_SNP [dm6]	T	C	5.751e^-5	1	INTRON chinmo
2L	10191623	2L_10191623_SNP [dm3] 2L_10191623_SNP [dm6]	A	T	5.786e^-5	1	SYNONYMOUS_CODING Sur UPSTREAM CG31874
2L	13918312	2L_13918312_SNP [dm3] 2L_13918312_SNP [dm6]	G	A	5.792e^-5	1	INTRON Ance-3
2R	2790068	2R_2790068_SNP [dm3] 2R_6902563_SNP [dm6]	T	C	5.792e^-5	1	INTRON CG30158
2R	14818751	2R_14818751_SNP [dm3] 2R_18931246_SNP [dm6]	G	A	5.793e^-5	1	INTRON sano
2L	1305455	2L_1305455_SNP [dm3] 2L_1305455_SNP [dm6]	A	T	5.834e^-5	1	INTERGENIC
2R	4151914	2R_4151914_SNP [dm3] 2R_8264409_SNP [dm6]	C	T	5.922e^-5	1	UTR_5_PRIME CG30376
2L	3920448	2L_3920448_SNP [dm3] 2L_3920448_SNP [dm6]	T	C	6.143e^-5	1	INTRON fred
2L	17796255	2L_17796255_SNP [dm3] 2L_17796255_SNP [dm6]	C	T	6.147e^-5	1	INTRON CadN2	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	14799211	3L_14799211_SNP [dm3] 3L_14806111_SNP [dm6]	G	A	6.336e^-5	1	INTRON CG17839
2L	11575016	2L_11575016_SNP [dm3] 2L_11575016_SNP [dm6]	G	C	6.504e^-5	1	INTERGENIC
3L	7299028	3L_7299028_SNP [dm3] 3L_7305928_SNP [dm6]	T	C	6.558e^-5	1	INTRON unc-13-4A
2L	1885997	2L_1885997_SNP [dm3] 2L_1885997_SNP [dm6]	G	T	6.669e^-5	1	INTRON CG7337	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	648329	2R_648329_SNP [dm3] 2R_4760824_SNP [dm6]	A	G	6.853e^-5	1	INTERGENIC	transposable element FlyBase
2R	648344	2R_648344_SNP [dm3] 2R_4760839_SNP [dm6]	A	T	6.853e^-5	1	INTERGENIC	transposable element FlyBase
2L	14844950	2L_14844950_SNP [dm3] 2L_14844950_SNP [dm6]	C	A	6.948e^-5	1	DOWNSTREAM CG15279 INTERGENIC
X	5591977	X_5591977_SNP [dm3] X_5697944_SNP [dm6]	A	G	6.949e^-5	1	UPSTREAM CG4096 DOWNSTREAM CR42794 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	7299038	3L_7299038_SNP [dm3] 3L_7305938_SNP [dm6]	T	C	6.970e^-5	1	INTRON unc-13-4A
3L	6334389	3L_6334389_INS [dm3] 3L_6341289_INS [dm6]	A	ATA	6.984e^-5	1	INTRON CG13300
X	11111129	X_11111129_SNP [dm3] X_11217096_SNP [dm6]	T	C	7.175e^-5	1	INTERGENIC

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By genomic position
Variant impact
Gene name

Microbiota_OTU012 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results