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=8.645e^-7)
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

Covariate	p-value	Significance
In_3R_K	0.0059940
In_3R_Mo	0.0689944

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_Mo	5.801	0.055

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1931 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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Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3L	18076321	3L_18076321_SNP [dm3] 3L_18083221_SNP [dm6]	G	A	6.460e^-7	0.512	INTRON CR43253	TF binding site mE1_TFBS_inv
2L	8371319	2L_8371319_INS [dm3] 2L_8371319_INS [dm6]	A	ATCTA	7.881e^-7	0.512	UPSTREAM CR45341 INTRON CG17292
2L	2025251	2L_2025251_SNP [dm3] 2L_2025251_SNP [dm6]	G	A	1.205e^-6	0.512	INTRON CG4238
X	13768849	X_13768849_SNP [dm3] X_13874816_SNP [dm6]	T	A	1.535e^-6	0.512	INTRON mamo
3L	10157038	3L_10157038_SNP [dm3] 3L_10163938_SNP [dm6]	T	C	1.543e^-6	0.512	INTRON dpr10
3L	9965563	3L_9965563_SNP [dm3] 3L_9972463_SNP [dm6]	G	T	1.705e^-6	0.512	UPSTREAM vnc & 2 others INTRON vnc & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_Ubx
2R	14475365	2R_14475365_SNP [dm3] 2R_18587860_SNP [dm6]	A	T	2.026e^-6	0.512	INTRON GEFmeso
3L	12306884	3L_12306884_SNP [dm3] 3L_12313784_SNP [dm6]	C	T	2.491e^-6	0.512	INTERGENIC
2R	11472329	2R_11472329_SNP [dm3] 2R_15584824_SNP [dm6]	T	A	2.519e^-6	0.512	INTERGENIC
X	10989728	X_10989728_SNP [dm3] X_11095695_SNP [dm6]	T	C	3.542e^-6	0.512	UPSTREAM CR45604 & 1 other DOWNSTREAM CG2061 INTERGENIC
2R	13383094	2R_13383094_SNP [dm3] 2R_17495589_SNP [dm6]	C	T	4.495e^-6	0.512	SYNONYMOUS_CODING CG30103	TF binding site mE1_TFBS_cad
3R	25378986	3R_25378986_SNP [dm3] 3R_29553264_SNP [dm6]	G	A	4.625e^-6	0.512	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_inv
2R	14475362	2R_14475362_INS [dm3] 2R_18587857_INS [dm6]	T	TA	4.630e^-6	0.512	INTRON GEFmeso
2R	14475380	2R_14475380_SNP [dm3] 2R_18587875_SNP [dm6]	A	T	4.674e^-6	0.512	INTRON GEFmeso
2R	14475381	2R_14475381_SNP [dm3] 2R_18587876_SNP [dm6]	G	T	4.674e^-6	0.512	INTRON GEFmeso
2R	14475386	2R_14475386_DEL [dm3] 2R_18587881_DEL [dm6]	AG	A	4.674e^-6	0.512	INTRON GEFmeso
2L	14082661	2L_14082661_SNP [dm3] 2L_14082661_SNP [dm6]	C	G	5.319e^-6	0.512	INTRON nAChRalpha5	TF binding site mE1_TFBS_zfh1
2R	13384470	2R_13384470_SNP [dm3] 2R_17496965_SNP [dm6]	G	C	5.470e^-6	0.512	DOWNSTREAM CG30103 INTERGENIC
3R	5911956	3R_5911956_SNP [dm3] 3R_10086234_SNP [dm6]	C	T	5.471e^-6	0.512	INTRON CR45054	TF binding site mE1_TFBS_Trl
2R	14345171	2R_14345171_SNP [dm3] 2R_18457666_SNP [dm6]	C	G	5.503e^-6	0.512	DOWNSTREAM CG30116 INTRON CG30116	TF binding site mE1_TFBS_HSA
2R	13385678	2R_13385678_SNP [dm3] 2R_17498173_SNP [dm6]	G	A	6.328e^-6	0.552	INTERGENIC
3L	13105164	3L_13105164_INS [dm3] 3L_13112064_INS [dm6]	T	TGTTCTCCAG	7.609e^-6	0.552	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3L	13105167	3L_13105167_SNP [dm3] 3L_13112067_SNP [dm6]	T	C	7.609e^-6	0.552	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
2L	12090463	2L_12090463_INS [dm3] 2L_12090463_INS [dm6]	C	CCATCAGC	7.741e^-6	0.552	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd mE1_TFBS_cad
2L	12167556	2L_12167556_SNP [dm3] 2L_12167556_SNP [dm6]	T	A	7.760e^-6	0.552	DOWNSTREAM ZnT33D INTRON CG31760
2L	8373705	2L_8373705_SNP [dm3] 2L_8373705_SNP [dm6]	G	A	8.156e^-6	0.552	SYNONYMOUS_CODING CG17292 UPSTREAM Wdr82	TF binding site mE1_TFBS_HSA
2L	18091693	2L_18091693_SNP [dm3] 2L_18091693_SNP [dm6]	G	A	9.114e^-6	0.552	SYNONYMOUS_CODING CG15153	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	18036428	3R_18036428_DEL [dm3] 3R_22210706_DEL [dm6]	GAGAAGGATG	G	9.561e^-6	0.552	INTRON SKIP
3R	18036473	3R_18036473_SNP [dm3] 3R_22210751_SNP [dm6]	G	A	9.561e^-6	0.552	INTRON SKIP
3R	18036501	3R_18036501_SNP [dm3] 3R_22210779_SNP [dm6]	T	C	9.561e^-6	0.552	INTRON SKIP
2L	15759696	2L_15759696_SNP [dm3] 2L_15759696_SNP [dm6]	G	A	9.747e^-6	0.552	SYNONYMOUS_CODING Gli	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	16641946	3R_16641946_SNP [dm3] 3R_20816224_SNP [dm6]	G	T	9.885e^-6	0.552	UPSTREAM Fancd2 DOWNSTREAM CG17270 INTERGENIC	TF binding site mE1_TFBS_jumu
3L	3849290	3L_3849290_SNP [dm3] 3L_3849290_SNP [dm6]	G	T	1.001e^-5	0.552	INTRON Awh	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	10260588	3L_10260588_INS [dm3] 3L_10267488_INS [dm6]	C	AA	1.064e^-5	0.552	UPSTREAM can INTERGENIC	regulatory region REDfly_CRMs
2L	21748597	2L_21748597_SNP [dm3] 2L_21748597_SNP [dm6]	G	T	1.101e^-5	0.552	INTRON step	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10332220	2R_10332220_SNP [dm3] 2R_14444715_SNP [dm6]	T	C	1.129e^-5	0.552	INTRON Oaz	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo
2L	22605766	2L_22605766_DEL [dm3] 2L_22713034_DEL [dm6]	TGCTACTA	T	1.161e^-5	0.552	INTRON CG40006
3L	3103557	3L_3103557_SNP [dm3] 3L_3103557_SNP [dm6]	G	T	1.220e^-5	0.552	INTRON Cht7
2R	13383753	2R_13383753_SNP [dm3] 2R_17496248_SNP [dm6]	A	T	1.242e^-5	0.552	DOWNSTREAM CG30103 INTERGENIC
2R	13384063	2R_13384063_SNP [dm3] 2R_17496558_SNP [dm6]	T	C	1.242e^-5	0.552	DOWNSTREAM CG30103 INTERGENIC
X	4614645	X_4614645_SNP [dm3] X_4720612_SNP [dm6]	T	A	1.264e^-5	0.552	INTRON Proc-R
2L	2553667	2L_2553667_SNP [dm3] 2L_2553667_SNP [dm6]	C	G	1.308e^-5	0.552	UPSTREAM CG3515 INTERGENIC
3L	5229784	3L_5229784_SNP [dm3] 3L_5236684_SNP [dm6]	A	T	1.334e^-5	0.552	DOWNSTREAM CG4669 INTRON shep
2L	3458744	2L_3458744_SNP [dm3] 2L_3458744_SNP [dm6]	C	G	1.358e^-5	0.552	SYNONYMOUS_CODING Sec5	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	13382078	2R_13382078_SNP [dm3] 2R_17494573_SNP [dm6]	G	A	1.391e^-5	0.552	NON_SYNONYMOUS_CODING CG30103
2R	13382079	2R_13382079_SNP [dm3] 2R_17494574_SNP [dm6]	G	A	1.391e^-5	0.552	NON_SYNONYMOUS_CODING CG30103
2R	14475376	2R_14475376_SNP [dm3] 2R_18587871_SNP [dm6]	T	A	1.394e^-5	0.552	INTRON GEFmeso
2L	3458525	2L_3458525_SNP [dm3] 2L_3458525_SNP [dm6]	A	G	1.532e^-5	0.594	SYNONYMOUS_CODING Sec5	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	2929604	2L_2929604_SNP [dm3] 2L_2929604_SNP [dm6]	G	A	1.644e^-5	0.601	INTRON lilli
X	4196608	X_4196608_SNP [dm3] X_4302575_SNP [dm6]	T	C	1.660e^-5	0.601	UPSTREAM CG12692 INTERGENIC
2R	14475357	2R_14475357_SNP [dm3] 2R_18587852_SNP [dm6]	T	A	1.677e^-5	0.601	INTRON GEFmeso
2L	4727566	2L_4727566_SNP [dm3] 2L_4727566_SNP [dm6]	C	T	1.815e^-5	0.601	INTERGENIC
2R	13381925	2R_13381925_SNP [dm3] 2R_17494420_SNP [dm6]	C	T	1.845e^-5	0.601	SYNONYMOUS_CODING CG30103
2R	13383774	2R_13383774_SNP [dm3] 2R_17496269_SNP [dm6]	C	T	1.845e^-5	0.601	DOWNSTREAM CG30103 INTERGENIC
2R	13383776	2R_13383776_SNP [dm3] 2R_17496271_SNP [dm6]	A	T	1.845e^-5	0.601	DOWNSTREAM CG30103 INTERGENIC
2R	13384238	2R_13384238_SNP [dm3] 2R_17496733_SNP [dm6]	G	T	1.845e^-5	0.601	DOWNSTREAM CG30103 INTERGENIC
2R	10271378	2R_10271378_SNP [dm3] 2R_14383873_SNP [dm6]	G	A	1.928e^-5	0.601	INTRON Dh44-R1	TF binding site BDTNP1_TFBS_da
2R	11472294	2R_11472294_SNP [dm3] 2R_15584789_SNP [dm6]	A	C	1.951e^-5	0.601	INTERGENIC
3L	13105160	3L_13105160_SNP [dm3] 3L_13112060_SNP [dm6]	A	T	1.972e^-5	0.601	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
2L	14244503	2L_14244503_SNP [dm3] 2L_14244503_SNP [dm6]	G	A	1.974e^-5	0.601	INTERGENIC
3L	3823388	3L_3823388_SNP [dm3] 3L_3823388_SNP [dm6]	T	C	2.027e^-5	0.601	INTRON enc	insulator Insulator_Class_II.mE01 TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3L	9968683	3L_9968683_SNP [dm3] 3L_9975583_SNP [dm6]	A	C	2.047e^-5	0.601	UTR_5_PRIME dpr6
2L	14082673	2L_14082673_SNP [dm3] 2L_14082673_SNP [dm6]	G	T	2.064e^-5	0.601	INTRON nAChRalpha5	TF binding site mE1_TFBS_zfh1
X	4196610	X_4196610_SNP [dm3] X_4302577_SNP [dm6]	T	C	2.086e^-5	0.601	UPSTREAM CG12692 INTERGENIC
3L	14281118	3L_14281118_SNP [dm3] 3L_14288018_SNP [dm6]	C	A	2.108e^-5	0.601	INTRON fz	TF binding site mE1_TFBS_cnc mE1_TFBS_HSA
2R	13381847	2R_13381847_SNP [dm3] 2R_17494342_SNP [dm6]	T	A	2.130e^-5	0.601	SYNONYMOUS_CODING CG30103
2L	12551106	2L_12551106_SNP [dm3] 2L_12551106_SNP [dm6]	A	C	2.180e^-5	0.605	INTERGENIC
2R	13114236	2R_13114236_SNP [dm3] 2R_17226731_SNP [dm6]	T	A	2.410e^-5	0.626	INTRON mbl
2L	3606086	2L_3606086_SNP [dm3] 2L_3606086_SNP [dm6]	C	G	2.510e^-5	0.626	NON_SYNONYMOUS_CODING odd	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl
X	4196619	X_4196619_SNP [dm3] X_4302586_SNP [dm6]	T	C	2.530e^-5	0.626	UPSTREAM CG12692 INTERGENIC
2R	20209542	2R_20209542_SNP [dm3] 2R_24322019_SNP [dm6]	G	C	2.575e^-5	0.626	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	13045781	2L_13045781_SNP [dm3] 2L_13045781_SNP [dm6]	T	C	2.612e^-5	0.626	INTRON CG9932
2L	8372336	2L_8372336_SNP [dm3] 2L_8372336_SNP [dm6]	C	A	2.637e^-5	0.626	UPSTREAM CG17292 INTRON CG17292
2L	6046439	2L_6046439_SNP [dm3] 2L_6046439_SNP [dm6]	A	G	2.638e^-5	0.626	UPSTREAM ade2 & 1 other DOWNSTREAM slmo & 1 other INTERGENIC
2L	10552126	2L_10552126_SNP [dm3] 2L_10552126_SNP [dm6]	A	G	2.655e^-5	0.626	INTRON Trim9	TF binding site mE1_TFBS_cad
3L	1780035	3L_1780035_SNP [dm3] 3L_1780035_SNP [dm6]	C	A	2.723e^-5	0.626	INTRON alpha-Spec	TF binding site mE1_TFBS_sens
3R	10785015	3R_10785015_DEL [dm3] 3R_14959293_DEL [dm6]	TA	T	2.746e^-5	0.626	INTERGENIC
2L	6041094	2L_6041094_SNP [dm3] 2L_6041094_SNP [dm6]	C	T	2.799e^-5	0.626	NON_SYNONYMOUS_CODING CG31643 DOWNSTREAM ade2
2L	9101403	2L_9101403_SNP [dm3] 2L_9101403_SNP [dm6]	G	T	2.861e^-5	0.626	INTERGENIC
2R	14471647	2R_14471647_SNP [dm3] 2R_18584142_SNP [dm6]	C	T	2.869e^-5	0.626	UPSTREAM GEFmeso INTRON GEFmeso	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	3823377	3L_3823377_SNP [dm3] 3L_3823377_SNP [dm6]	T	C	3.045e^-5	0.626	INTRON enc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2R	11993048	2R_11993048_SNP [dm3] 2R_16105543_SNP [dm6]	A	T	3.065e^-5	0.626	INTRON Rho1
3R	21910770	3R_21910770_SNP [dm3] 3R_26085048_SNP [dm6]	G	A	3.127e^-5	0.626	INTRON dys	TF binding site mE1_TFBS_HSA
2R	17408739	2R_17408739_SNP [dm3] 2R_21521234_SNP [dm6]	A	G	3.149e^-5	0.626	NON_SYNONYMOUS_CODING CG30289 UPSTREAM CG30288
3L	6817532	3L_6817532_SNP [dm3] 3L_6824432_SNP [dm6]	G	C	3.239e^-5	0.626	INTERGENIC	regulatory region REDfly_CRMs
3L	10116256	3L_10116256_SNP [dm3] 3L_10123156_SNP [dm6]	C	T	3.241e^-5	0.626	INTRON dpr6
X	4651773	X_4651773_SNP [dm3] X_4757740_SNP [dm6]	T	C	3.283e^-5	0.626	INTERGENIC
2R	14471645	2R_14471645_INS [dm3] 2R_18584140_INS [dm6]	A	AT	3.325e^-5	0.626	UPSTREAM GEFmeso INTRON GEFmeso	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	2553644	2L_2553644_SNP [dm3] 2L_2553644_SNP [dm6]	T	A	3.379e^-5	0.626	UPSTREAM CG3515 INTERGENIC
3R	7810943	3R_7810943_SNP [dm3] 3R_11985221_SNP [dm6]	G	A	3.388e^-5	0.626	SYNONYMOUS_CODING mfas UPSTREAM CG3397	TF binding site mE1_TFBS_cad mE1_TFBS_inv
2R	1375477	2R_1375477_SNP [dm3] 2R_5487972_SNP [dm6]	C	T	3.404e^-5	0.626	INTRON CG30440
2L	8501820	2L_8501820_DEL [dm3] 2L_8501820_DEL [dm6]	CCCAC	C	3.433e^-5	0.626	INTRON Dh31
2L	2025882	2L_2025882_SNP [dm3] 2L_2025882_SNP [dm6]	T	A	3.453e^-5	0.626	INTRON CG4238
2R	10332217	2R_10332217_SNP [dm3] 2R_14444712_SNP [dm6]	T	G	3.466e^-5	0.626	INTRON Oaz	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo
2R	10332219	2R_10332219_SNP [dm3] 2R_14444714_SNP [dm6]	C	G	3.466e^-5	0.626	INTRON Oaz	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo
2L	9426473	2L_9426473_SNP [dm3] 2L_9426473_SNP [dm6]	A	T	3.523e^-5	0.626	UPSTREAM Fbp2 DOWNSTREAM Mco1 INTERGENIC
2L	973086	2L_973086_SNP [dm3] 2L_973086_SNP [dm6]	A	G	3.531e^-5	0.626	INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	16764707	2R_16764707_SNP [dm3] 2R_20877202_SNP [dm6]	A	T	3.546e^-5	0.626	INTRON Ipk1
3L	10123911	3L_10123911_SNP [dm3] 3L_10130811_SNP [dm6]	T	C	3.562e^-5	0.626	INTRON dpr6
2R	19976557	2R_19976557_SNP [dm3] 2R_24089034_SNP [dm6]	A	T	3.580e^-5	0.626	SYNONYMOUS_CODING snama

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By genomic position
Variant impact
Gene name

Microbiota_OTU014 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results